Mouse arrays and kits comprising the same

Abstract

Mouse arrays and methods for their use are provided. The subject arrays include a plurality of polynucleotide spots, each of which is made up of a polynucleotide probe composition of unique polynucleotides corresponding to a key mouse gene. The subject arrays find use in hybridization assays, particularly in assays for the identification of differential gene expression of key mouse genes of interest.

Description

INTRODUCTION

1. Technical Field

The field of this invention is biopolymeric arrays.

2. Background of the Invention

"Biochips" or arrays of binding agents, such as oligonucleotides and peptides, have become an increasingly important tool in the biotechnology industry and related fields. These binding agent arrays, in which a plurality of binding agents are deposited onto a solid support surface in the form of an array or pattern, find use in a variety of applications, including drug screening, nucleic acid sequencing, mutation analysis, and the like. One important use of biochips is in the analysis of differential gene expression, where the expression of genes in different cells, normally a cell of interest and a control, is compared and any discrepancies in expression are identified. In such assays, the presence of discrepancies indicates a difference in the classes of genes expressed in the cells being compared.

In methods of differential gene expression, arrays find use by serving as a substrate to which is bound nucleic acid "probe" fragments. One then obtains "targets" from analogous cells, tissues or organs of a healthy and diseased organism. The targets are then hybridized to the immobilized set of nucleic acid "probe" fragments. Differences between the resultant hybridization patterns are then detected and related to differences in gene expression in the two sources.

A variety of different array technologies have been developed in order to meet the growing need of the biotechnology industry, as evidenced by the extensive number of patents and references listed in the relevant literature section below.

Despite the wide variety of array technologies currently in preparation or available on the market, there is a continued need to identify new array devices to meet the needs of specific research applications.

Relevant Literature

Patents and patent applications describing arrays of biopolymeric compounds and methods for their fabrication include: U.S. Pat. Nos. 5,242,974; 5,384,261; 5,405,783; 5,412,087; 5,424,186; 5,429,807; 5,436,327; 5,445,934; 5,472,672; 5,527,681; 5,529,756; 5,545,531; 5,554,501; 5,556,752; 5,561,071; 5,599,895; 5,624,711; 5,639,603; 5,658,734; 5,700,637; 5,744,305; 5,770,456; WO 93/17126; WO 95/11995; WO 95/35505; EP 742 287; and EP 799 897.

Patents and patent application describing methods of using arrays in various applications include: U.S. Pat. Nos. 5,143,854; 5,288,644; 5,324,633; 5,432,049; 5,470,710; 5,492,806; 5,503,980; 5,510,270; 5,525,464; 5,547,839; 5,580,732; 5,661,028; WO 95/21265; WO 96/31622; WO 97/10365; WO 97/27317; EP 373 203; and EP 785 280.

Other references of interest include: Atlas Human cDNA Expression Array I (April 1997) CLONTECHniques XII: 4-7; Lockhart et al., Nature Biotechnology (1996) 14: 1675-1680; Shena et al., Science (1995) 270: 467-470; Schena et al., Proc. Nat'l Acad. Sci. USA (1996)93:10614-10619; Shalon et al., Genome Res. (1996) 6: 639-645; Milosavljevic et al., Genome Res. (1996) 6:132-141; Nguyen et al., Genomics (1995)29: 207-216; Pietu et al., Genome Res. (1996) 6: 492-503; Zhao et al., Gene (1995) 166:207-213; Chalifour et al., Anal. Biochem. (1994) 216:299-304; Heller et al., Proc. Nat'l Acad. Sci. USA (1997) 94: 2150-2155; and Schena, M., BioAssays (1996) 18: 427-431.

SUMMARY OF THE INVENTION

Mouse arrays and kits including the same, as well as methods for their preparation and use in hybridization assays, are provided. The subject arrays have a plurality of probe polynucleotide spots each made up of a unique polynucleotide(s) that corresponds to a key mouse gene of interest. The subject arrays find use in the expression analysis of key mouse genes.

DEFINITIONS

The term "nucleic acid" as used herein means a polymer composed of nucleotides, e.g. deoxyribonucleotides or ribonucleotides.

The terms "ribonucleic acid" and "RNA" as used herein means a polymer composed of ribonucleotides.

The terms "deoxyribonucleic acid" and "DNA" as used herein means a polymer composed of deoxyribonucleotides.

The term "oligonucleotide" as used herein denotes single stranded nucleotide multimers of from about 10 to 100 nucleotides in length.

The term "polynucleotide" as used herein refers to single or double stranded polymer composed of nucleotide monomers of greater than about 120 nucleotides in length up to about 1000 nucleotides in length.

"Key mouse genes" and "key mouse related genes" are those genes that have been identified by those of skill in the art to play primary roles in a variety of different biological processes. Typically the mouse genes represented on the array are genes that are under tight transcriptional control. Key mouse genes of interest that may be represented on the array include: oncogenes, cell cycle genes, apoptosis genes, growth factor genes, cytokine genes, interleukin genes, receptor genes, and genes associated with different stages of embryonic development. Preferably, the key mouse genes are genes that are well characterized, i.e. at least genes in which at least the partial sequence is known and the function of the expression product of the gene is at least partially understood. Specific key mouse genes of interest include those listed in Table 1, infra. A gene is considered to be the same as a gene listed in Table 1 even if it: (a) has a different name or accession number in a gene sequence database, e.g. GENBANK; (b) has at least 90% homology (as determined using the FASTA program with default settings) to the sequence of one of the GENBANK accession numbers listed in Table 1; or (c) belongs to the same gene cluster as defined in NCBI in Unigene database available on the World Wide Web.

The "unique" polynucleotide sequences of each probe spot on the arrays of the subject invention are distinctive or different with respect to every other unique polynucleotide sequence on the arrays that corresponds to a key mouse gene, as that term is defined herein. In other words, for at least 80% of the genes on the array, and more usually at least 90% of the genes on the array, any two different unique polynucleotides corresponding to a key mouse gene on the array, (i.e. any two unique polynucleotides taken from different, non-identical spots on the array), are not homologous. By not homologous is meant that the sequence identity between the two given unique polynucleotides is less than about 90%, usually less than about 85% and more usually less than about 80% as measured by the FASTA program using default settings. Moreover, each polynucleotide sequence on the array is statistically chosen to ensure that the probability of homology to any sequence of that type is very low. Morever, each unique sequence on the array is statistically chosen to insure that probability of homology to any other known sequence associated with key mouse genes is very low, whether or not the other sequence is represented on the array. An important feature of the individual polynucleotide probe compositions of the subject arrays is that they are only a fragment of the entire cDNA of the key mouse gene to which they correspond. In other words, for each gene represented on the array, the entire cDNA sequence of the gene is not represented on the array. Instead, the sequence of only a portion or fragment of the entire cDNA is represented on the array by this unique polynucleotide.

The term "polynucleotide probe composition" refers to the nucleic acid composition that makes up each of the probe spots on the array that correspond to a particular key mouse gene. Thus, the term `polynucleotide probe composition` includes nucleic acid compositions of unique polynucleotides but excludes control or calibrating polynucleotides (e.g. polynucleotides corresponding to housekeeping genes) which may also be present on the array, as described in greater detail infra. The polynucleotide compositions are made up of single stranded polynucleotides (i.e. polynucleotides that are not hybridized to each other), where all of the polynucleotides in the probe composition may be identical to each other or there may be two or more different polynucleotides (i.e. polynucleotides of different nucleotide sequence) in each probe composition, e.g. where the two different polynucleotides are complementary to each other.

DESCRIPTION OF THE SPECIFIC EMBODIMENTS

Mouse arrays, as well as methods for their preparation and use, are provided. In the subject mouse arrays, a plurality of polynucleotide probe spots is stably associated with the surface of a solid support. Each different polynucleotide probe spot is made up of a unique polynucleotide that corresponds to a key mouse gene of interest. The subject arrays find particular use in gene expression assays of key mouse genes. In further describing the subject invention, the mouse arrays themselves are first discussed, followed by a description of methods for their preparation. Next, a review of representative applications in which the subject arrays may be employed is provided.

It is to be understood that the invention is not limited to the particular embodiments of the invention described below, as variations of the particular embodiments may be made and still fall within the scope of the appended claims. It is also to be understood that the terminology employed is for the purpose of describing particular embodiments, and is not intended to be limiting. Instead, the scope of the present invention will be established by the appended claims.

In this specification and the appended claims, the singular forms "a," "an," and "the" include plural reference unless the context clearly dictates otherwise. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this invention belongs.

Arrays of the Subject Invention-General Description Array Structure

The arrays of the subject invention have a plurality of polynucleotide probe spots stably associated with a surface of a solid support. Each probe spot on the array comprises a polynucleotide probe sample or polynucleotide probe composition of known identity, usually of known sequence, as described in greater detail below. The polynucleotide probe spots on the array may be any convenient shape, but will typically be circular, elliptoid, oval, annular, or some other analogously curved shape, where the shape may, in certain embodiments, be a result of the particular method employed to produce the array. The density of the all of the spots on the solid surface, i.e. both probe spots and non-probe spots, e.g. calibration spots, control spots, etc., is at least about 5/cm.sup.2 and usually at least about 10/cm.sup.2 but does not exceed about 1000/cm.sup.2, and in many embodiments does not exceed about 500/cm.sup.2, where in certain preferred embodiments, the density does not exceed about 400/cm.sup.2, usually does not exceed about 300/cm.sup.2, and more usually does not exceed about 60/cm.sup.2. The spots may be arranged in any convenient pattern across or over the surface of the array, such as in rows and columns so as to form a grid, in a circular pattern, and the like, where generally the pattern of spots will be present in the form of a grid across the surface of the solid support.

In the subject arrays, the spots of the pattern are stably associated with the surface of a solid support, where the support may be a flexible or rigid solid support. By stably associated is meant that the polynucleotides of the spots maintain their position relative to the solid support under hybridization and washing conditions. As such, the polynucleotide members which make up the spots can be non-covalently or covalently stably associated with the support surface. Examples of non-covalent association include non-specific adsorption, binding based on electrostatic (e.g. ion, ion pair interactions), hydrophobic interactions, hydrogen bonding interactions, specific binding through a specific binding pair member covalently attached to the support surface, and the like. Examples of covalent binding include covalent bonds formed between the spot polynucleotides and a functional group present on the surface of the rigid support, e.g. --OH, where the functional group may be naturally occurring or present as a member of an introduced linking group, as described in greater detail below.

The array is present on either a flexible or rigid substrate. By flexible is meant that the support is capable of being bent, folded or similarly manipulated without breakage. Examples of solid materials which are flexible solid supports with respect to the present invention include membranes, flexible plastic films, and the like. By rigid is meant that the support is solid and does not readily bend, i.e. the support is not flexible. As such, the rigid substrates of the subject arrays are sufficient to provide physical support and structure to the polymeric targets present thereon under the assay conditions in which the array is employed, particularly under high throughput handling conditions. Furthermore, when the rigid supports of the subject invention are bent, they are prone to breakage.

The solid supports upon which the subject patterns of spots are present in the subject arrays may take a variety of configurations ranging from simple to complex, depending on the intended use of the array. Thus, the substrate could have an overall slide or plate configuration, such as a rectangular or disc configuration. In many embodiments, the substrate will have a rectangular cross-sectional shape, having a length of from about 10 mm to 200 mm, usually from about 40 to 150 mm and more usually from about 75 to 125 mm and a width of from about 10 mm to 200 mm, usually from about 20 mm to 120 mm and more usually from about 25 to 80 mm, and a thickness of from about 0.01 mm to 5.0 mm, usually from about 0.1 mm to 2 mm and more usually from about 0.2 to 1 mm.

The substrates of the subject arrays may be fabricated from a variety of materials. The materials from which the substrate is fabricated should ideally exhibit a low level of non-specific binding during hybridization events. In many situations, it will also be preferable to employ a material that is transparent to visible and/or UV light. For flexible substrates, materials of interest include: nylon, both modified and unmodified, nitrocellulose, polypropylene, and the like, where a nylon membrane, as well as derivatives thereof, is of particular interest in this embodiment. For rigid substrates, specific materials of interest include: glass; plastics, e.g. polytetrafluoroethylene, polypropylene, polystyrene, polycarbonate, and blends thereof, and the like; metals, e.g. gold, platinum, and the like; etc.

The substrates of the subject arrays comprise at least one surface on which the pattern of probe spots is present, where the surface may be smooth or substantially planar, or have irregularities, such as depressions or elevations. The surface on which the pattern of spots is present may be modified with one or more different layers of compounds that serve to modify the properties of the surface in a desirable manner. Such modification layers, when present, will generally range in thickness from a monomolecular thickness to about 1 mm, usually from a monomolecular thickness to about 0.1 mm and more usually from a monomolecular thickness to about 0.001 mm. Modification layers of interest include: inorganic and organic layers such as metals, metal oxides, polymers, small organic molecules and the like. Polymeric layers of interest include layers of: peptides, proteins, polynucleic acids or mimetics thereof, e.g. peptide nucleic acids and the like; polysaccharides, phospholipids, polyurethanes, polyesters, polycarbonates, polyureas, polyamides, polyethyleneamines, polyarylene sulfides, polysiloxanes, polyimides, polyacetates, and the like, where the polymers may be hetero- or homopolymeric, and may or may not have separate functional moieties attached thereto, e.g. conjugated.

The total number of probe spots on the substrate will vary depending on the number of different polynucleotide probes one wishes to display on the surface, as may be desired depending on the particular application in which the subject arrays are to be employed. Generally, the pattern present on the surface of the array will comprise at least about 10 distinct spots, usually at least about 20 distinct spots, and more usually at least about 50 distinct spots, where the number of spots may be as high as 10,000 or higher, but will usually not exceed about 5,000 distinct spots, and more usually will not exceed about 3,000 distinct spots. In many embodiments, it is preferable to have each distinct probe composition presented in duplicate, i.e. so that there are two spots for each distinct polynucleotide probe composition of the array. In certain embodiments, the number of spots will range from about 400 to 1200, usually from 500 to 1200.

In the arrays of the subject invention (particularly those designed for use in high throughput applications, such as high throughput analysis applications), a single pattern of spots may be present on the array or the array may comprise a plurality of different spot patterns, each pattern being as defined above. When a plurality of different spot patterns are present, the patterns may be identical to each other, such that the array comprises two or more identical spot patterns on its surface, or the spot patterns may be different, e.g. in arrays that have two or more different types of target nucleic acids represented on their surface, e.g an array that has a pattern of spots corresponding to key mouse genes and a pattern of spots corresponding to another type or category of mouse genes, such as mouse stress genes. Where a plurality of spot patterns are present on the array, the number of different spot patterns is at least 2, usually at least 6, more usually at least 24 or 96, where the number of different patterns will generally not exceed about 384.

Where the array comprises a plurality of spot patterns on its surface, preferably the array comprises a plurality of reaction chambers, wherein each chamber has a bottom surface having associated therewith an pattern of spots and at least one wall, usually a plurality of walls surrounding the bottom surface. Such array configurations and the preparation thereof is further described in U.S. patent application Ser. No. 08/974,298 filed on Nov. 19, 1997, the disclosure of which is herein incorporated by reference. Of particular interest in many embodiments are arrays in which the same pattern of spots in reproduced in 24 or 96 different reaction chambers across the surface of the array.

Within any given pattern of spots on the array, there may be a single spot that corresponds to a given target or a number of different spots that correspond to the same target, where when a plurality of different spots are present that correspond to the same target, the probe compositions of each spot that corresponds to the same target may be identical of different. In other words, a plurality of different targets are represented in the pattern of spots, where each target may correspond to a single spot or a plurality of spots, where the probe composition among the plurality of spots corresponding to the same target may be the same or different. Where a plurality of spots (of the same or different composition) corresponding to the same target is present on the array, the number of spots in this plurality will be at least about 2 and may be as high as 10, but will usually not exceed about 5. The number of different targets represented on the array is at least about 2, usually at least about 10 and more usually at least about 20, where in many embodiments the number of different targets, e.g. genes, represented on the array is at least about 50. The number of different targets represented on the array may be as high as 1000 or higher, but will usually not exceed about 800 and more usually will not exceed about 700. In a preferred embodiment, the number of different targets represented on the array ranges from about 400 to 800, an usually from about 500 to 7000. A target is considered to be represented on an array if it is able to hybridize to one or more probe compositions on the array.

The amount of polynucleotide present in each spot will be sufficient to provide for adequate hybridization and detection of target nucleic acid during the assay in which the array is employed. Generally, the amount of polynucleotide in each spot will be at least about 0.1 ng, usually at least about 0.5 ng and more usually at least about 1 ng, where the amount may be as high as 1000 ng or higher, but will usually not exceed about 20 ng and more usually will not exceed about 10 ng. The copy number of each polynucleotide in a spot will be sufficient to provide enough hybridization sites for target molecule to yield a detectable signal, and will generally range from about 0.01 fmol to 50 fmol, usually from about 0.05 fmol to 20 fmol and more usually from about 0.1 fmol to 5 fmol. Where the spot has an overall circular dimension, the diameter of the spot will generally range from about 10 to 5,000 .mu.m, usually from about 20 to 2,000 ,.mu.m and more usually from about 50 to 1000 .mu.m.

A critical feature of the subject arrays is that all of the probe polynucleotide spots of the array correspond to key mouse genes of interest, particularly genes that have been identified by those of skill in the art to play primary roles in a variety of different biological processes of the mouse. Typically the mouse genes represented on the array are genes that are under tight transcriptional control. As such, each polynucleotide probe spot on the array will correspond to a key mouse gene of interest. Each probe spot on the array may correspond to a different key mouse gene. Alternatively, two or more, usually no more than four, and more usually no more than three, different probe spots may correspond to the same key mouse gene, i.e. a key mouse gene may be represented by one or a plurality of different probe spots on the array. Furthermore, any given key mouse gene may be represented by two or more identical probe spots on the array, e.g. a particular probe spot may be presented on the array once or in duplicate, triplicate, etc, as mentioned above. The number of different key mouse genes represented on the array may vary, where generally the number of different key mouse genes represented on the array will range from about 50 to 1000, usually from about 100 to 700 and more usually from about 300 to 700. A key mouse gene is considered to be represented on a given array if a target nucleic acid derived from the key mouse gene is able to hybridize to at least one probe spot on the array. Key mouse genes that may be represented on the arrays include: oncogenes, cell cycle genes, apoptosis genes, growth factor genes, cytokine genes, interleukin genes, receptor genes, genes associated with different stages of embryonic development, and the like. In certain embodiments, of particular interest is an array having the following types of genes represented on its surface: oncogenes & tumor suppressors; cell cycle regulators; stress response proteins; ion channel & transport proteins; intracellular signal transduction modulators & effectors; apoptosis-related proteins; DNA synthesis, repair & recombination proteins; transcription factors & general DNA binding proteins; growth factor & chemokine receptors; interleukin & interferon receptors, hormone receptors; neurotransmitter receptors; cell-surface antigens & cell adhesion proteins; interleukins & interferons; cytoskeleton & motility proteins; and protein turnover. Specific key mouse genes that may be represented on the arrays of the subject invention include those listed in Table 1, infra. In many preferred embodiments, the subject mouse arrays will include at least 20, usually at least 50 and more usually at least 100 of the genes listed in Table 1 (i.e. at least 20, usually at least 50 and more usually at least 100 of the genes listed in Table 1 are represented on the array), where in certain preferred embodiments, all of the genes listed in Table 1 are present on the array. In a particularly preferred embodiment, the array is made up of polynucleotide probes having a sequence that is identical to and/or complementary to, or at least partially includes, each of the specific gene regions listed in Col. 3 of Table 1.

The average length of the probe polynucleotides on the array is chosen to be of sufficient length to provide a strong and reproducible signal, as well as tight and robust hybridization. As such, the average length of the polynucleotides of the array will typically range from about 120 to 1000 nt and usually from about 150 to 800 nt, where in many embodiments, the average length ranges from about 200 to 700 nt, and usually 200 to 600 nt. The length of each polynucleotide on the array is less than the length of the mRNA to which it corresponds. As such, the polynucleotide represents only a fraction of the full length cDNA to which it corresponds.

The polynucleotide probe compositions that make up each spot on the array will be substantially, usually completely, free of non-nucleic acids, i.e. the probe compositions will not comprise non-nucleic acid biomolecules found in cells, such as proteins, lipids, and polysaccharides. In other words, the oligonucleotide spots of the arrays are substantially, if not entirely, free of non-nucleic acid cellular constituents. By substantially free is meant that the probe composition is at least about 90%, usually at least about 95% and more usually at least about 98% dry weight nucleic acid.

The polynucleotide probes may be nucleic acid, e.g. RNA, DNA, or nucleic acid mimetics, e.g. such as nucleic acids comprising non-naturally occurring heterocyclic nitrogenous bases, peptide-nucleic acids, locked nucleic acids (see Singh & Wengel, Chem. Commun. (1998) 1247-1248); and the like. Nucleic acid mimetics that may be polynucleotide probes on the present arrays include nucleic acids chemically modified from the native phosphodiester structure in order to increase their intracellular stability and binding affinity. A number of such modifications have been described in the literature which alter the chemistry of the backbone, sugars or heterocyclic bases. Among useful changes in the backbone chemistry are phosphorothioates; phosphorodithioates, where both of the non-bridging oxygens are substituted with sulfur; phosphoroamidites; alkyl phosphotriesters and boranophosphates. Achiral phosphate derivatives include 3'-O'-5'-S-phosphorothioate, 3'-S-5'-O-phosphorothioate, 3'-CH.sub.2 -5'-O-phosphonate and 3'-NH-5'-O-phosphoroamidate. Peptide nucleic acids replace the entire ribose phosphodiester backbone with a peptide linkage. Sugar modifications are also used to enhance stability and affinity. The .alpha.-anomer of deoxyribose may be used, where the base is inverted with respect to the natural .beta.-anomer. The 2'-OH of the ribose sugar may be altered to form 2'-O-methyl or 2'-O-allyl sugars, which provides resistance to degradation without comprising affinity. Modification of the heterocyclic bases must maintain proper base pairing. Some useful substitutions include deoxyuridine for deoxythymidine; 5-methyl-2'-deoxycytidine and 5-bromo-2'-deoxycytidine for deoxycytidine. 5-propynyl-2'-deoxyuridine and 5-propynyl-2'-deoxycytidine have been shown to increase affinity and biological activity when substituted for deoxythymidine and deoxycytidine, respectively.

As mentioned above, the subject arrays typically comprise one or more additional spots of polynucleotides which are not key mouse genes. Other spots which may be present on the substrate surface include spots comprising genomic DNA, housekeeping genes, negative and positive control genes, and the like. These latter types of spots comprise polynucleotides that are not "unique" as that term is defined and used herein, i.e. they are "common." In other words, they are calibrating or control genes whose function is not to tell whether a particular "key" mouse gene of interest is expressed, i.e. whether a particular key mouse gene is expressed in a particular sample, but rather to provide other useful information, such as background or basal level of expression, and the like. For example, spots comprising genomic DNA may be provided in the array, where such spots may serve as orientation marks. Spots comprising plasmid and bacteriophage genes, genes from the same or another species which are not expressed and do not cross hybridize with the cDNA target, and the like, may be present and serve as negative controls. Specific negative controls of interest include: M13 mp18(+) strand DNA, lambda DNA and pUC 18. In addition, spots comprising housekeeping genes and other control genes from the same or another species may be present, which spots serve in the normalization of mRNA abundance and standardization of hybridization signal intensity in the sample assayed with the array. Specific housekeeping genes of interest include: ubiquitin, phospholipase A2, hypoxanthine-guanine phosphoribosyl transferase, glyceraldehyde 3-phosphate dehydrogenase, tubulina alpha, HLA class I histocompatibility antigen, C-4 alpha chain, beta-actin, 23 kDa highly basic protein and ribosomal protein S9.

Polynucleotide Probes of the Arrays

Each probe spot of the pattern present on the surface of the substrate is made up of a unique polynucleotide probe composition. By "polynucleotide probe composition" is meant a collection or population of single stranded polynucleotides capable of participating in a hybridization event under appropriate hybridization conditions, where each of the individual polynucleotides may be the same--have the same nucleotide sequence--or have different sequences, for example the probe composition may consist of 2 different single stranded polynucleotides that are complementary to each other (i.e. the two different polynucleotides in the spot are complementary but physically separated so as to be single stranded, i.e. not hybridized to each other). In many embodiments, the probe compositions will comprise two complementary, single stranded polynucleotides.

In the polynucleotide probe compositions, the sequence of the polynucleotides are chosen so that each distinct unique polynucleotide does not cross-hybridize with any other distinct unique polynucleotide of another probe spot on the array, i.e. the polynucleotide of any other polynucleotide composition that corresponds to a key mouse gene. As such, the nucleotide sequence of each unique polynucleotide of a probe composition will have less than 90% homology, usually less than 85% homology, and more usually less than 80% homology with any other different polynucleotide of a probe composition of the array, where homology is determined by sequence analysis comparison using the FASTA program using default settings. The sequence of unique polynucleotides in the probe compositions are not conserved sequences found in a number of different genes (at least two), where a conserved sequence is defined as a stretch of from about 40 to 200 nucleotides which have at least about 90% sequence identity, where sequence identity is measured as above. The polynucleotide will generally be a deoxyribonucleic acid having a length of from about 120 to 1000, usually from 120 to 700 nt, and more usually 200 to 600 nt. The polynucleotide will not cross-hybridize with any other polynucleotide on the array under standard hybridization conditions. Again, the length of the polynucleotide will be shorter than the mRNA to which it corresponds.

Array Preparation

The subject arrays can be prepared using any convenient means. One means of preparing the subject arrays is to first synthesize the polynucleotides for each spot and then deposit the polynucleotides as a spot on the support surface. The polynucleotides may be prepared using any convenient methodology, such as automated solid phase synthesis protocols, restriction digestion of a gene fragment insert cloned into a vector, preparative PCR and like, where preparative PCR or enzymatic synthesis is preferred in view of the length and the large number of polynucleotides that must be generated for each array. In the case of automated solid phase synthesis, each polynucleotide can be represented by several overlapping or non-overlapping oligonucleotides from 10 to 100 nucleotides in length, which cover all or a partial sequence of a gene or polynucleotide. See U.S. patent application Ser. No. 60/104,179, the disclosure of which is herein incorporated by reference.

For preparative PCR, primers flanking either side of the portion of the gene of interest will be employed to produce amplified copy numbers of the portion of interest. Methods of performing preparative PCR are well known in the art, as summarized in PCR, Essential Techniques (Ed. J. F. Burke, John Wiley & Sons) (1996). Alternatively, if a gene fragment of interest is cloned into a vector, vector primers can be used to amplify the gene fragment of interest to produce the polynucleotide.

In determining the portion of the gene to be amplified and subsequently placed on the array, regions of the gene having a sequence unique to that gene should preferably be amplified. Different methods may be employed to choose the specific region of the gene to be amplified. Thus, one can use a random approach based on availability of a gene of interest. However, instead of using a random approach which is based on availability of a gene of interest, a rational design approach may also be employed to choose the optimal sequence for the hybridization array. Preferably, the region of the gene that is selected and amplified is chosen based on the following criteria. First, the sequence that is chosen should yield a polynucleotide that does not cross-hybridize with any other polynucleotide that is present on the array. Second, the sequence should be chosen such that the polynucleotide has a low probability of cross-hybridizing with a polynucleotide having a nucleotide sequence found in any other gene, whether or not the gene is to be represented on the array. As such, sequences that are avoided include those found in: highly expressed gene products, structural RNAs, repeated sequences found in the sample to be tested with the array and sequences found in vectors. A further consideration is to select sequences which provide for minimal or no secondary structure, structure which allows for optimal hybridization but low non-specific binding, equal or similar thermal stabilities, and optimal hybridization characteristics.

The prepared polynucleotides may be spotted on the support using any convenient methodology, including manual techniques, e.g. by micro pipette, ink jet, pins, etc., and automated protocols. See U.S. Pat. No. 5,770,151 and WO 95/35505, the disclosures of which are herein incorporated by reference, for discussions of representative ways of spotting polynucleotides on a support. Of particular interest is the use of an automated spotting device, such as the Beckman Biomek 2000 (Beckman Instruments). As mentioned above, the polynucleotide probe compositions that are spotted onto the array surface are made up of single stranded polynucleotides, where all the polynucleotides may be identical to each other or a population of complementary polynucleotides may be present in each spot.

Methods of Using the Subject Arrays

The subject arrays find use in a variety of different applications in which one is interested in detecting the occurrence of one or more binding events between target nucleic acids and probes on the array and then relating the occurrence of the binding event(s) to the presence of a target(s) in a sample, i.e. the expression of a particularkey mouse gene in a sample. In general, the device will be contacted with the sample suspected of containing the target key mouse gene under conditions sufficient for binding of any target present in the sample to a complementary polynucleotide present on the array. Generally, the sample will be a fluid sample and contact will be achieved by introduction of an appropriate volume of the fluid sample onto the array surface, where introduction can via inlet port, deposition, dipping the array into a fluid sample, and the like.

Generation of Labeled Target

Targets may be generated by methods known in the art. mRNA can be labeled and used directly as a target, or converted to a labeled cDNA target. Generally, such methods include the use of oligonucleotide primers. Primers that may be employed include oligo dT, random primers, e.g. random hexamers and gene specific primers, as described in U.S. patent application Ser. No. 08/859,998, the disclosure of which is herein incorporated by reference. Where gene specific primers are employed, the gene specific primers are preferably those primers that correspond to the different polynucleotide spots on the array. Thus, one will preferably employ gene specific primers for each different polynucleotide that is present on the array, so that if the gene is expressed in the particular cell or tissue being analyzed, labeled target will be generated from the sample for that gene. In this manner, if a particular key mouse gene present on the array is expressed in a particular sample, the appropriate target will be generated and subsequently identified.

A variety of different protocols may be used to generate the labeled target nucleic acids, as is known in the art, where such methods typically rely on the enzymatic generation of the labeled target using the initial primer. Labeled primers can be employed to generate the labeled target. Alternatively, label can be incorporated during first strand synthesis or subsequent synthesis, labeling or amplification steps in order to produce labeled target. Representative methods of producing labeled target are disclosed in U.S. patent application Ser. No. 08/859,998, the disclosure of which is herein incorporated by reference. Alternatively, the label can be introduced by chemical cDNA synthesis.

Hybridization and Detection

As mentioned above, following preparation of the target nucleic acid from the tissue or cell of interest, the labeled target nucleic acid is then contacted with the array under hybridization conditions, where such conditions can be adjusted, as desired, to provide for an optimum level of specificity in view of the particular assay being performed. Suitable hybridization conditions are well known to those of skill in the art and reviewed in Maniatis et al, supra and WO 95/21944, e.g. stringent conditions (e.g. at 50.degree. C. or higher and 0.1XSSC (15 mM sodium chloride/01.5 mM sodium citrate). In analyzing the differences in the population of labeled target nucleic acids generated from two or more physiological sources using the arrays described above, each population of labeled target nucleic acids are separately contacted to identical probe arrays or together to the same array under conditions of hybridization, preferably under stringent hybridization conditions, such that labeled target nucleic acids hybridize to complementary probes on the substrate surface.

Where all of the target sequences comprise the same label, different arrays will be employed for each physiological source (where different could include using the same array at different times). Alternatively, where the labels of the targets are different and distinguishable for each of the different physiological sources being assayed, the opportunity arises to use the same array at the same time for each of the different target populations. Examples of distinguishable labels are well known in the art and include: two or more different emission wavelength fluorescent dyes, like Cy3 and Cy5, two or more isotopes with different energy of emission, like .sup.32 p and .sup.33 p, light scattering particles with different scattering spectra, labels which generate signals under different treatment conditions, like temperature, pH, treatment by additional chemical agents, etc., or generate signals at different time points after treatment. Using one or more enzymes for signal generation allows for the use of an even greater variety of distinguishable labels, based on different substrate specificity of enzymes (alkaline phosphatase/peroxidase).

Following hybridization, non-hybridized labeled nucleic acid is removed from the support surface conveniently by washing, generating a pattern of hybridized nucleic acid on the substrate surface. A variety of wash solutions are known to those of skill in the art and may be used.

The resultant hybridization patterns of labeled nucleic acids may be visualized or detected in a variety of ways, with the particular manner of detection being chosen based on the particular label of the target nucleic acid, where representative detection means include scintillation counting, autoradiography, fluorescence measurement, calorimetric measurement, light emission measurement, light scattering and the like.

Following detection or visualization, the hybridization patterns may be compared to identify differences between the patterns. Where arrays in which each of the different probes corresponds to a known gene are employed, any discrepancies can be related to a differential expression of a particular gene in the physiological sources being compared.

Utility

The subject methods find use in differential mouse gene expression assays. As such, the mouse arrays of the subject invention find use in a variety of different applications, where such applications include: profiling differential gene expression in transgenic knockout mice or other experimental mouse models; investigating processes such as embryo genesis and tumorigenesis; discovering potential therapeutic and diagnostic drug targets; and the like.

Kits

Also provided are kits for performing analyte binding assays using the subject devices, where kits for carrying out differential gene expression analysis assays are preferred. Such kits according to the subject invention will at least comprise a mouse array according to the subject invention. The kits may further comprise one or more additional reagents employed in the various methods, such as primers for generating target nucleic acids, dNTPs and/or rNTPs, which may be either premixed or separate, one or more uniquely labeled dNTPs and/or rNTPs, such as biotinylated or Cy3 or Cy5 tagged dNTPs, or other post synthesis labeling reagent, such as chemically active derivatives of fluorescent dyes, biotin, digoxigenin, or strept/avidin-label conjugate or antibody-label conjugate, enzymes, such as reverse transcriptases, DNA polymerases, and the like, various buffer mediums, e.g. hybridization and washing buffers, labeled target purification reagents and components, like spin columns, etc., signal generation and detection reagents, e.g streptavidin-alkaline phosphatase conjugate, chemifluorescent or chemiluminescent substrate, and the like.

The following examples are offered by way of illustration and not by way of limitation.

EXPERIMENTAL

EXAMPLE 1

Generation of Mouse cDNA array

588 cDNA fragments corresponding to 588 different mouse key genes as listed in Table 1 were amplified from quick-clone cDNA (CLONTECH) in 588 separate test tubes using a combination of sense and antisense gene-specific primers capable of amplifying the specific gene fragments of interest as specified in Table 1. Amplification was conducted in a 100-.mu.l volume containing 2 .mu.l of mixture of 10 Quick-clone cDNA from placenta, brain, liver, lung, leukocytes, spleen, skeletal muscle, testis, kidney and ovary (CLONTECH), 40 mM Tricine-KOH (pH 9.2 at 22.degree. C.), 3.5 mM Mg(OAc).sub.2, 10 mM KOAc, 75 .mu.g/ml BSA, 200 .mu.M of each dATP, dGTP, dCTP and dTTP, 0.2 .mu.M of each sense and antisense gene-specific primers and 2 .mu.l of KlenTaq Polymerase mix. Temperature parameters of the PCR reactions were as follows: 1 min at 95.degree. C. followed by 20-35 cycles of 95.degree. C. for 15 sec and 68.degree. C. for 2 min; followed by a 10-min final extension at 68.degree. C. PCR products were examined on 1.2% agarose/EtBr gels in 1.times. TBE buffer. As a DNA size marker a 1 Kb DNA Ladder was used. ds cDNA was then precipitated by addition of a half volume of 4M ammonium acetate (about 35 .mu.l) and 3.7 volumes of 95% ethanol (about 260 .mu.l). After vortexing, the tube was immediately centrifuged at 14,000 r.p.m. in a microcentrifuge for 20 min. The pellet was washed with 80% ethanol without vortexing, centrifuged as above for 10 min, air dried, and dissolved in 10 .mu.l of deionized water. Yield of ds cDNA after the amplification step was about 5 .mu.g. The ds cDNA fragments for all 588 genes were cloned into pAtlas 1A-cloning vector (Clontech) using blunt end ligation by T4 DNA polymerase and identity of the clones was confirmed by sequence analysis. The ds cDNA inserts with the sequence corresponding 588 genes were amplified by PCR using a combination of antisense and sense gene-specific primers, as described above. The ds cDNA was denatured by adding 1 .mu.l of 10X denaturing solution (1 M NaOH, 10 mM EDTA) and incubating at 65.degree. C. for 20 min. All cDNA probes were transferred in 384-well plate and loaded on positively charged nylon membrane (Schleher & Schull) using 384 pin tool and Biomek 2000 (Beckman) robot.

The resultant array has 588 different key mouse genes represented on it. The specific key mouse genes represented on the array are listed in Table 1. Also provided in Table 1 is the specific region of each gene that is represented on the array. See Col. 3 of Table 1. Thus, Table 1 also provides the sequence for each polynucleotide probe on the array. For example, the array comprises a polynucleotide probe to MmRad 51, where the probe has a DNA sequence that is either complementary or identical to the sequence of the mRNA from the 855-1199 nucleotide of the sense strand counting from the 5' end of the mRNA sequence, where the entire sequence has been deposited in GENBANK under accession no. D13473 and is therefore readily available.

TABLE 1______________________________________ FRAGMENT LENGTH, bpGENE NAME GENBANK # (start-end)______________________________________MmRad51; yeast DNA repair protein DT3473 855-1199Rad51 and E coli RecA homologueInterleukin-8 receptor D17630 664-1022Catenin alpha D25281 1276-1594BST-l; lymphocyte differentiation D31788 674-1014antigen CD38Oncostatin M D31942 1017-1360CSA receptor L05630 841-1165Heparin-binding EGF-like growth L07264 258-673factor (Diphtheria toxin receptor)Fms-related tyrosine kinase 3 U04807 46-418Flt3/Flk2 ligandCD27; lymphocyte-specific NGF L24495 596-846receptor family memberFibroblast growth factor receptor M28998 200-583Basic (b FGF-R)Granulocyte colony - stimulatings M58288 251-529factor receptorGrowth/ diffferentiation factor 1 M62301 2267-2566(GDF-1) (TGF- beta family)PKC-delta; protein kinase C delta M69042 1740-2011typeGA binding protein beta-2 chain M74517 613-931CD 40L receptor(TNF receptor M83312 417-754family)Fasl receptor (Fas antigen, Apo-1 M83649 416-736antigen)Interleukin 12 (p40) beta chain M86671 652-963Vascular endothelial growth factor M95200 688-955(VEGF)Interleukin 11 (adipogenesis U03421 196-475inhibitory factor)Interleukin 15 U14332 605-1057LIMK; LIM serine/threonine kinase U15159 1376-1699DAD-1; defender against cell death 1 U83628 221-509CD 30L receptor (Lymphocyte U25416 135-435activation antigene CD 30, Ki-1antigene)Mast cell factor U44725 79-417C-C cheynokine receptor (Monocyte U56819 965-1262chemoattractant protein 1 receptor(MCP-1RA)Leukemia inhibitory factor (LIF) X06381 63-366(cholinergic differentiation factor)Intercellular adhesion molecule-1 X52264 1053-1385Interleukin-1 receptor type II X59769 882-1134Corticotropin releasing factor X72305 1411-1748receptorHepatocyte growth factor X72307 641-965(hepapoitein)Keratinocyte growth factor FGF-7 Z22703 63-325Activin type I receptor Z31663 847-1130Transcription factor TF II D D01034 291-556ZO-1; Tight junction protein; discs- D14340 3714-4001large family member, partiallyhomologous to a dIg-A tumorsuppressor in Drosophila/ERCC5 excision repair protein; D16306 1336-1639DNA-repair protein complementingXP-G cells (XPG)Bax; Bcl-2 heterodimerization L22472 172-534partner and homologueB7-2; T lymphocyte activation L25606 570-967antigen CD86; CD28 antigen ligand2, B7-2 antigen; alternative CTLA4counter-receptorNF2; Merlin (moesin-ezrin-radixin- L27105 2175-2400like protein); shwannomin, murineneurofibromatosis type 2susceptibility proteinPim-1 proto-oncogene M13945 2713-2930Egr-1 Zn-finger regulatory protein M20157 399-753PKC-alpha; protein kinase C alpha M25811 1566-1924typeCD44 antigen M27129 789-1141T-lymphocyte activated protein M31042 285-606Neuronal-cadherin (N-cadherin) M31131 1212-1409ATP-dependent DNA helicase II 70 M38700 274-632kDa subunit; thyroid Ku (p70/p80)autoantigen p70 subunit; p70 Ku)G13; G-alpha-13 guanine nucleotide M63660 2057-2377regulatory proteinTranscription factor RelB M83380 1456-1728Vascular cell adhesion protein 1 M84487 984-1304ERCC3 DNA repair helicase; DNA- S71186 1147-1444repair protein complementing XP-Bcells (XPBC)CRE-BP1; cAMP response element S76657 412-748binding protein 1XRCC1 DNA-repair protein, U02887 900-1183affecting ligationNuclear hormone receptor ROR- U53228 368-675ALPHA-114-3-3 protein eta U57311 374-640Prothymosin alpha X56135 186-455PAX-8 (paired box protein PAX 8) X57487 680-1011CamK IV; Ca2/calmodulin- X58995 1269-1608dependent protein kinase IV(catalytic chain)ATP-dependent DNA helicase II 80 X66323 565-875kDa subunit; thyroid Ku (p70/p80)autoantigen p80 subunit; p80 Ku)Ret proto-oncogene (Papillary X67812 2359-2680thyroid carcinoma-encoded protein)Nm23-M2; nucleoside diphosphate X68193 80-454kinase B; metastasis-reducingprotein;. c-myc-related transcriptionfactorMAPKK6; MAP kinase kinase X97052 375-7116(dual specificity) (MKK6)DNA polymerase alpha catalytic D17384 563-908subunit (p180)Caspase-3; Nedd2 cysteine protease D28492 398-694(positive regulator of programmedcell death ICH-1 homologue)PSD-95/SAP90A D50621 1512-1889Angiotensin-converting enzyme L04946 850-1113(ACE) (clone ACE.5.)Clusterin; complement lysis L08235 515-744inhibitor; testosterone-repressedprostate message 2; apolipoprotein J;sulfated glycoprotein-2Adipocyte differentiation-associated L12721 404-709proteinEpidermal growth factor receptor L21671 1562-1873kinase substrate EPS8Jak3 tyrosine-protein kinase; Janus L33768 3123-3426kinase 3Desmocollin 2 L33779 1317-1691Stat6; signal transducer and activator L47650 2057-2411of transcription 6; IL-4 Stat; STA6Lymphocyte-specific tyrosine- M12056 1205-1488protein kinase LCKERA-1 Protein (ERA-1-993) M22115 723-1062Homeo Box protein 2.1 (Hox-2.1) M26283 647-884Zinc finger X-chromosomal protein M32309 2153-2554(ZFX)WTI; Wilms tumor protein; tumor M55512 1262-1563suppressorTristetraproline M57422 262-504Nucleobindin M96823 80-357PAX-5 (B cell specific transcription M97013 286-629factor)IFNgR2; interferon-gamma receptor S69336 832-1089second (beta) chain; interferongamma receptor accessory factor-1(AF-1)Transcriptional enhancer factor 1 S74227 934-1233(TEF-1)Transcription factor NFAT 1, U02079 1601-1910isoform, alphaDNA-binding protein SATB1 U05252 1101-1380CCHB3; calcium channel (voltage- U20372 351-639gated; dihydropyridine-sensitive; L-type) beta-3 subunit)p57kip2; cdk-inhibitor kip2 (cyclin- U20553 989-1272dependent kinase inhibitor 1 B)member of the p21CIP1 Cdkinhibitor family; candidate tumorsuppressor genesnoN; ski-related oncogene U36203 671-1006Homeo Box protein 7.1 (Hox-7.1) X14759 740-992Neuronal cell surface protein F3 X14943 1033-1311GATA-3 transcription factor X55123 858-1125YB1 DNA binding protein X57621 550-873Dipeptidyl peptidase iv X58384 61-294Fli-1 ets-related proto-oncogene X59421 267-623RXR-beta cis-11-retinoic acid X66224 1225-1477receptorC3H cytochrome P450; Cyp1b1 X78445 295-593Ubiquitin-conjugating enzyme, yeast X96859 51-392Rad6 homologue; murine HR6BRelaxin Z27088 51-365Transcription factor LIM-1 Z27410 1673-1934DNA topoisornerase I (Top I) D10061 1051-1357DNA topoisomerase II (Top II) D12513 520-870GST Pi 1; glutathione S-transferase D30687 62-369Pi 1; preadipocyte growth factorGlutathione S-transferase A J03958 54-311Glutathione S-transferase Mu 1 J04696 13-263c-Ab1 proto-oncogene L10656 878-1145A-Raf proto-oncogene M13071 1042-1320c-Src proto-oncogene M17031 452-758Retinoic acid binding protein II M35523 276-571cellular (CRABP-II)Cyclin D2 (G1/S-specific) M83749 781-1074Cyclin D3 (G1/S-specific) U43844 484-7905-Hydroxytryptamine receptor S49542 400-707[Serotonin receptor type 2 (SHT2)]Cyclin D1 (G1/S-specific) S78355 1858-2205Pur-alpha transcriptional activator; U02098 1082-1309sequence-specific ssDNA-bindingproteinCdc2Sa; cdc2SMl; MPI1 (M-phase U27323 606-986inducer phosphatase 1)ERCC-1; DNA excision repair X07414 189-484proteinc-rel proto-oncogene X15842 1729-2064Inhibin alpha subunit X69618 810-1117Glutathione reductase X76341 115-377Insulin-like growth factor binding X81581 474-719protein-3 (IGFBP-3)Cyclin A (G2/M-specific) Z26580 701-1009Preproglucagon Z46845 172-531NF-kB p65; NF-kappa-B M61909 101-363transcription factor p65 subunit; rel-related polypeptidePKC-theta; protein kinase C theta D11091 658-957typeVLA-3 alpha subunit D13867 288-589NADPH-cytochrome P450 reductase D17571 326-605Beta-protachykinin a D17584 273-523Wee1/p87; cdc2 tyrosine 15-kinase D30743 1816-2159Protein tyrosine phosphatase D83966 1060-1426Jun-D; c-jun-related transcription J05205 737-964factorIntegrin alpha 7 L23423 2399-2713Gadd45; growth arrest and DNA- L28177 144-434damage-inducible proteinBcl-xL apoptosis regulator (bcl-x L35049 641-906long); BcI-2 family memberN-myc proto-oncogene protein X03919 3262-3450cAMP-dependent protein kinase type M20473 538-750I-beta regulatory chainIRF1; interferon regulatory factor 1 M21065 1-233HSP86; heat shock 86kD protein M36830 255-551LFA-1 alpha; integrin alpha L; M60778 1838-2050leukocyte adhesion glycoproteinLFA-1 alpha chain; antigen CD11A(p180)APC; Adenomatous Polyposis Coli M88127 4127-4476proteinCdc2Sb; cdc2SM2; MPI2 (M-phase S93521 1893-2200inducer phosphatase 2)P13-K p110; phosphatidylinositol 3- U03279 1437-1723kinase catalytic subunitRSP27; heat shock 27kD protein 1 U03560 245-500Csk; c-Src-kinase and negative U05247 645-984regulatorFasl; Fas antigen ligand; generalized U06948 168-488lymphoproliferation disease gene(gld) in miceMAPK; MAP kinase; p38 U10871 465-780p19ink4; cdk4 and cdk6 inhibitor U19597 228-516Elf-1 Ets family transcription factor U19617 1585-1902CRAF1; TNF receptor (CD40 U21050 1225-1466receptor) associated factor; TRAF-relatedSPI3; serpin; similar to human U25844 915-1230proteinase inhibitor 6 (placentalthrombin inhibitor) serine proteinaseinhibitorRIP cell death protein; Fas/APO-1 U25995 1945-2223(CD95) interactor, contains deathdomainSLAP; src-like adapter protein; Eck U29056 109-427receptor tyrosine kinase-associatedAtm; ataxia telangiectasia murine U43678 8989-9170homologueEB1 APC-binding protein U51196 607-834TANK; I-TRAF; TRAF family U51907 135-437member associated NF-kB activatorCaspase-11; ICH-3 cysteine U59463 352-686protease; upstream regulator of ICEMLHI DNA mismatch repair U59883 1037-1278protein; MutL homologueInsulin-like growth factor-IA X04480 183-406Cell surface glycoprotein MAC-1 X07640 1892-2179alpha subunitN-ras proto-oncogene; transforming X13664 548-857G-proteinL-myc proto-oncogene protein X13945 5287-5590CD18 antigen beta subunit X14951 1366-1706(leukocyte adhesion LFA-1) (CD3,P150, 95)c-Fgr proto-oncogene X52191 1305-1538Integrin alpha 4 X53176 2176-2449PKC-beta; protein kinase C beta-II X53532 1712-2089typeHSP60; heat shock 60 kDa protein 1 X53584 1432-1691(chaperonin, GroEL homologue);mitochondrial matrix protein P1c-Cbl proto-oncogene (Adaptor X57111 858-1151protein)Cdc25 phosphatase; guanine X59868 942-1276nucleotide releasing proteinEzrin; Villin 2; NF-2 (merlin) related X60671 1571-1812filament/plasma membraneassociated proteinCyclin B1 (G2/M-specific) X64713 1184-1447Integrin alpha 6 X69902 261-6115-Hydroxytryptamine (serotonin) X72395 1422-1711receptor 3Homeobox protein HOXD-3 X73573 141-362Cyclin E (G1/S-specific) X75888 799-1140MAPKAPK-2; MAp kinase- X76850 719-987activated protein kinase; MAPKAPkinase 2Fra-2 (fos-related antigen 2) X83971 617-844Cyclin A1 (G2/M-specific) X84311 656-916DCC; netrin receptor; X85788 4193-4508immunoglobulin gene superfamilymember; former tumor suppressorprotein candidateMHR23A; Rad23 UV excision repair X92410 613-955protein homologue; xerodemiapigmentosum group C (XPC) repaircomplementing proteinMHR23B; Rad23 UV excision repair X92411 542-807protein homologue; xerodermapigmentosum group C (XPC) repaircomplementing proteinIntegrin beta Y00769 1990-2320MmRad52; yeast DNA repair protein Z32767 159-417Rad52 homologueCyclin G-(G2/M-specific) Z37110 300-619Prostaglandin E2 receptor EP4 D13458 1146-1442subtypeInterleukin-5 receptor D90205 1389-1739Epidermal growth factor (EGF) J00380 180-505Erythropoietin receptor J04843 1193-1377Insulin receptor J05149 653-1011p53; tumor suppressor; DNA- K01700 1125-1517binding proteinCf2r; coagulation factor II L03529 762-1154(thrombin) receptorPTPRG; protein-tyrosine L09562 1248-1504phosphatase gammaDNA-binding protein SMBP2 L10075 4790-5088Interleukin-10 receptor L12120 1762-2110Interleukin-2 receptor gamma chain L20048 1073-1313Bone morphogenetic protein 1 L24755 2402-2676Uromodulin L33406 1809-2136Thrombopoietin L34169 652-954Transforming growth factor beta M13177 772-1075Granulocyte colony- stimulating M13926 86-377factor (G-CSF)Neuroleukin M14220 1110-1490Insulin-like growth factor-2 M14951 46-328(somatomedin A)Interleukin 1 beta M15131 827-1225c-myb proto-oncogene protein M16449 1212-1513Tumor necrosis factor beta TNF-beta M16819 461-805(Lymphotoxin-alpha)Interleukin-1 receptor M20658 2050-2410CSF-1; M-CSF; colony stimulating X05010 1268-1657factor-1Interleukin-4 receptor (membrane- M27959 2469-2705bound form)Interferon-gamma receptor M28233 1262-1550Interleukin-7 receptor M29697 701-1104Gamma interferon induced monokine M34815 42-323(MIG)Interleukin 10 M37897 175-456NF-kappa B binding subunit (nuclear M57999 3122-3417factor) (TFDB5)Tumor necrosis factor receptor 1; M59378 1961-2376TNFR-1PDGFRa; platelet-derived growth M84607 474-803factor alpha-receptorInterleukin-9 receptor M84746 795-1086iNOS1; nitric oxide synthase M87039 3178-3455(inducible)Interferon alpha-beta receptor M89641 808-1120Activating transcription factor 4 M94087 416-769(mATF4)Beta2-RAR; retinoic acid receptor S56660 589-896beta-2Tie-2 proto-oncogene S67051 1843-2179IGF-I-R alpha; insulin-like growth U00182 489-885factor I receptor alpha subunitIGFR II; insulin-like growth factor U04710 707-1060receptor II, cation-independentmannose-6-P receptor; elevated inWilms's tumor cellsStat3; APRF; acute phase response U06922 1575-1910factorCalcitonin receptor 1b U18542 1375-1630Endothelin b receptor [Ednrb] U32329 379-695Prepro-endothelin-3 U32330 703-1008Pre-platelet-derived growth factor X04367 2336-2677receptorCD 4 receptor (T cell activation X04836 1652-1877antigene)Interleukin 7 X07962 241-496Macrophage inflamatory protein X12531 25-359Thrombomodulin X14432 1082-1365Interleukin 6 (B cell differentiation X51975 1638-1898factor)Androgen receptor X53779 2189-2491Bone morphogenetic protein 4 X56848 1275-1513(BMP-4) (TGF-beta family)Transferrin receptor protein (p90, X57349 654-1023CD71)Transforming growth factor beta 2 X57413 2227-2541Glutamate receptor, ionotropic X57497 1290-1657AMPAITNF 55; tumor necrosis factor 1 X57796 656-1022(55kd)Mdm2; pS3-regulating protein X58876 1364-1646Transcription factor 1 for heat shock X61753 203-570geneCD40L; CD40 ligand X65453 545-809c-Fms proto-oncogene (macrophage X68932 2399-2686colony stimulating factor 1 (CSF-1)receptor)B-myb proto-oncogene; myb-related X70472 2109-2456protein BEar-2; v-erbA related proto- X76654 1065-1376oncogeneTie-1 tyrosine-protein kinase X80764 1425-1844receptorGlutamate receptor, ionotropic D10651 506-786NMDA2B (epsilon 2)Glutamate receptor, ionotropic D10217 3966-4209NMDA2A (epsilon 1)CD7 antigen D10329 28-421Transcription factor S-II D00926 518-767(transcription elongation factor)Basic Fibroblast growth factor (b- D12482 290-620FGF)Bone morphogenetic protein receptor D16250 1454-1837G-protein-coupled receptor D17292 833-1115Transcription factor SP2 D17407 734-1079CdkS; cyclin-dependent kinase 5 D29678 552-882TGF-beta receptor type 1 D25540 1407-1629Kinesin like protein KIF 3B D26077 3519-3722Kinesin family protein KIF1A D29951 2553-2830Fibroblast growth factor 9 D38258 91-379Neuronal death protein D83698 627-805Syp; SR-PTP2; adaptor protein D84372 1229-1543tyrosine phosphataseInterferon regulatory factor 2 (IRF 2) J03168 718-976Lamimin receptor 1 J02870 368-675NF-IB protein (transcription factor) D90176 452-791Jun-B; c-jun-related transcription J03236 514-740factorTissue plasminogen activator J03520 622-1020Romeo Box protein 4.2 (Rox-4.2) J03770 565-945Nur77 early response protein; J04113 825-1059thyroid hormone (TR3) receptorEts-2 transcription factor J04103 917-1281c-Jun proto-oncogene (transcription J04115 951-1238factor AP-1 component)Serine protease inhibitor homolog J6 J05609 581-855Nerve growth factor beta (beta-NGF) K01759 642-901Cdk4; cyclin-dependent kinase 4 L01640 230-616Acetylcholine receptor delta subunit K02582 1400-1655MAPKK1; MAP kinase kinase 3 L02526 1284-1583(dual specificity) (MKK1)GABA-A transporter 4 L04662 960-1341GABA-A transporter 3 L04663 1010-1320Vegfr1; Vascular endothelial growth L07297 1144-1541factor receptor 1/Fms-relatedtyrosine kinase 1 (Flt1)Adrenergic receptor, beta 1 L10084 404-772Eph3 (Nuk) tyrosine-protein kinase L25890 2255-2491receptorMTJ1; DnaJ-like heat-shock protein L16953 1059-1384from mouse tumorTTMP-3 tissue inhibitor of L19622 274-592metalloproteinases-3Insulin receptor substrate-1 (IRS-1) L24563 1027-1304YY1 (UCRBP) transcriptional factor L13968 1052-1292Interleukin-converting enzyme (TCE) L28095 30-269Hepatoma transmembrane kinase L38847 927-1219ligandVoltage-gated sodium channel L36179 4179-4505Bad; heterodimeric partner for Bcl- L37296 1079-1375XL and Bcl-2; promotes cell deathJnk stress-activated protein kinase L35236 795-1032(SAPK)Cytoskeletal epidermal keratin (18 M11686 473-773human)Nerve growth factor alpha (alpha- M11434 294-494NGF)Epidermal keratin (1 human) M10937 326-683Nicotinic acetylcholine receptor M14537 1226-1568MDR1; P-glycoprotein; multidrug M14757 1500-1886resistance protein; efflux pumpCD2 antigen M18934 354-602Homeo Box protein 1.1 (Hox-1.1) M17192 466-723Fetal myosin alkali light chain M19436 205-504Interleukin 4 M25892 77-310Rb; pp105; Retinoblastoma M26391 2036-2296susceptibility-associated protein(tumor suppressor gene; cell cycleregulator)Rsk; ribosomal protein S6 kinase M28489 1191-1436Pletelet- derived growth factor (A M29464 152-425chain) (PDGF- A)Cytoskeletal epidermal keratin (19 M28698 194-500human)RAG-1; V(D)J recombination M29475 2155-2404activating proteinInterleukin-3 receptor M29855 1975-2254K-fibroblast growth factor M30642 309-577Octamer binding transcription factor M34381 774-999(Oct 3)Plasminogen activator inhibitor M33960 1096-1344CD3 antigen, delta polypeptide M33158 73-361Homeo Box protein 2.5 (Hox-2.5) M34857 11-277HSP84; heat shock 84kD protein M36829 342-736Mast cell protease (MMCP) - 4 M55617 634-992Erk1; extracellular signal-regulated M61177 115-373kinase 1; p44; Ert2P13-K p85; phosphatidylinositol 3- M60651 981-1260kinase regulatory subunit;phosphoprotein p85; PDGF signalingpathway memberp58/GTA; galactosyltransferase M58633 1022-1284associated protein kinase (cdc2-related protein kinase)Serine protease inhibitor 2 (spi-2) M64086 1499-1754B-Raf proto-oncogene M64429 1651-2036Etkl (Mek4; HEK) tyrosine-protein M68513 2681-2915kinase receptor HEKRAG-2; V(D)J recombination M64796 671-944activating proteinCollagenase type IV M84324 696-1040Interleukin-6 receptor beta chain; M83336 1423-1741membrane glycoprotein gp130Alpha cardiac myosin heavy chain M76601 2094-2391Retinoic acid receptor RXR- gamma M84819 701-1082Granulocyte-macrophage colony- M85078 904-1289stimulating factor receptor.GABA-A receptor alpha-1 submit M86566 1251-1606Endothelial ligand for L-selectin M93428 182-541(GLYCAM 1)Integrin beta 7 subunit M95633 2142-2423DNAse I U00478 665-871Cortactin; protein tyrosine kinase U03184 426-653substrateAdenosine A2M2 receptor U05672 491-735DNA ligase I U04674 1678-2054Adenosine A1M receptor U05671 302-673Non-muscle myosin light chain 3 U04443 84-370Cathepsin H U06119 325-694Stat1; signal transducer and activator U06924 1749-2104of transcriptionp21/Cip1/Waf1; cdk-inhibitor protein U09507 9-403Cdk7; MO15; cyclin-dependent U11822 454-824kinase 7 (homologue of XenopusMO15 cdk-activating kinase)p27kipl; G1 cyclin-Cdk protein U10440 270-454kinase inhibitor, p21-relatedGem; induced, immediate early U10551 220-471protein; Ras family memberVRL; Von Hippel-Lindau tumor U12570 885-1111suppressor proteinCek 5 receptor protein tyrosine U12983 1037-1287kinase ligandGlutathione peroxidase (plasma U13705 766-1046protein); selenoprotein.Integrin alpha 5 (CD51) U14135 2170-2516Ski proto-oncogene U14173 707-1037Ablphilin-I (abi-1) similar to U17698 351-585HOXD3BAG-1; bcl-2 binding protein with U17162 17-334anti-cell death activityShc transforming adaptor protein; U15784 1220-1451Src homology 2 (SR2) protein, SRB-relatedMAPKK4; MAP kinase kinase 4; U18310 1380-1749Jnk activating kinase 1; (JNKK1;SEK1; MKK4)Transcription factor LRG - 21 U19118 618-966Interferon inducible protein 1 U19119 1342-1636A20 zinc finger protein; apoptosis U19463 1952-2293inhibitorp18ink4; cdk4 and cdk6 inhibitor U19596 16-284I-kB (I-kappa B) beta U19799 419-778Dv12; dishevelled-2 tissue polarity U24160 1205-1578proteinNuclear factor related to P45 NF-E2 U20532 1429-1759MSH2 DNA mismatch repair U21011 2150-2490protein; MutS homologue 2GapIII; GTPase-activating protein U20238 328-644Syk tyrosine-protein kinase U25685 1235-1524(activated p21cdc42Rs kinase (ack))p107; RBL1; Retinoblastoma gene U27177 1973-2365product-related protein p107 (cellcycle regulator)PMS2 DNA mismatch repair protein; U28724 749-1013yeast PMSI homolog 2Limphotoxin receptor (TNFR U29173 1415-1668family)BRCA1; Breast/ovarian cancer U31625 5126-5430susceptibility locus 1 productPm1; Murine homologue of the U33626 1667-2064leukemia-associated PML geneTransducin beta-2 subunit U34960 515-834I-kB (I-kappa B) alpha chain U36277 541-823TRAIL; TNF-related apoptosis U37522 981-1288inducing ligand; Apo-2 ligandp130; Retinoblastoma gene product- U36799 970-1321related protein Rb2/p130 (cell cycleregulator)CACCC Box- binding protein BKLF U36340 826-1065FAF1; Fas-associated protein factor, U39643 423-681apoptosis activatorZinc finger transcription factor RU49 U41671 1229-1591GTBP; G/T-mismatch binding U42190 1477-1769protein; MSH6.PLC beta; phospholipase C beta 3 U43144 1933-2271Frizzled-3; Drosophila tissue polarity U43205 2037-2285gene frizzled homologue 3;dishevelled receptorMAPKK3; MAP kinase kinase 3 U43187 1436-1742(dual specificity) (MKK3, MEK3)Myelobiastin; trypsin-chymotrypsin U43525 503-807related serine proteaseZinc finger Kruppel type Zfp 92 U47104 578-896TDAG51; couples TCR signaling to U44088 729-1042Fas (CD95) expressionPOU domain, class 2, associated U43788 610-884factor 1ALG-2; calcium binding protein U49112 527-861required for programmed cell deathUnconventional myosin VI U49739 3784-4021Transcription factor CTCF (11 zinc U51037 1625-1911fingers)Transcription factor C 1 U53925 3895-4227Madrl; mSmadl; Mothers against U58992 238-476dpp protein (Mad) murinehomologue; TGF-beta signalingprotein-1 (bsp-1); candidate tumorsuppressor geneBcl-W apoptosis regulator; Bcl-2 U59746 153-368family memberMad related protein 2 (MADR2) U60530 584-820Cyclin C (G1-specific) U62638 714-986Mph-1 nuclear transcriptional U63386 1621-1884repressor for hox genesRad50; DNA repair protein U66887 1383-1707Fyn proto-oncogene; Src family U70324 584-882memberc-myc proto-oncogene protein X01023 379-667c-Fos proto-oncogene; transcription V00727 482-734factor AP-1 component fos cellularoncogeneCathepsin L X06086 267-588Glutamate receptor channel subunit X04648 41-408gammac-Fes proto-oncogene X12616 2342-2598Cytotoxic cell protease 2 (B10) X12822 439-686Homeo Box protein 3.1 (Hox-3.1) X07439 449-722Homeo Box protein 2.4 (Hox-2.4) X13721 1949-2284Fos-B; c-fos-related protein fos B X14897 920-1278Plasminogen activator inhibitor-2 X16490 674-978c-ErbA oncogene; thyroid hormone X51983 400-675receptor.Cathepsin D X53337 587-894Vimentin X51438 868-1096HMG-14 non histone chromosomal X53476 643-1017proteinMacrophage inflamatory protein 2 X53798 14-352alpha (MIP 2 alpha)Bone morphogenetic protein 7 X56906 670-971(BMP-7) (osteogenic protein 1)Transcription factor SP1P X56959 866-1128(POUdomain transcription factor)Homeo Box protein 8 (Hox-8) X59252 826-1132Fibroblast growth factor receptor 4 X59927 2446-2820Rac1 murine homologue X57277 425-651Transcription factor UBF X60831 689993Kinesin heavy chain X61435 1898-2182CCAAT- Binding transcription X61800 904-1150factor(C/EBP)TIMP-2 tissue inhibitor of X62622 1236-1468metalloproteinases-2Ets-related protein PEA 3 X63190 1702-2040Vav; GDP-GTP exchange factor; X64361 1083-1351proto-oncogenePAX-6 (paired box protein) X63963 1081-1325Cyclin B2 (G2/M-specific) X66032 874-1236Chop10; murine homologue of X67083 17-332Gadd153 (growth arrest and DNA-damage-inducible protein)PD-1 possible cell death inducer; Ig X67914 1481-1734gene superfamily memberInhibin beta A subunit (TGF beta X69619 1064-1304family)Vegfr2; KDR/flk1 vascular X70842 1394-1721endothelial growth factor tyrosinekinase receptorProtease nexin 1 (PN-1) X70296 746-985MRE-binding transcription factor X71327 552-916Activator-1 140 KD subunit X72711 4137-4375(replication factor C 140KD)DP-1 (DRTF-polipeptide 1) cell X72310 925-1305cycle regulatory transcription factor5-Hydroxytryptamine (serotonin) X72230 982-1314receptor 1cGelatinase B X72795 599-954XPAC; xeroderma pigmentosum X74351 447-669group A correcting proteinIntegrin alpha 2 (CD49b) X75427 1595-1976Growth/diffferentiation factor 2 X77113 939-1329(GDF-2)Insulin-like growth factor binding X81582 781-1140protein-4 (IGFBP-4)Insulin-like growth factor binding X81579 27-256protein-1 (IGFBP-1)IGFBP-2; Insulin-like growth factor X81580 449-817binding protein 2; autocrine and/orparacrine growth promoterInsulin-like growth factor binding X81583 461-824protein-5 (IGFBP-5)Insulin-like growth factor binding X81584 701-1039protein-6 (IGFBP 6)A-myb proto-oncogene; myb-related X82327 1017-1334protein AMembrane type matrix X83536 877-1101matalloproteinaseElk-1 ets-related proto-oncogene X87257 1498-1680E2F-5 transcription factor X86925 426-728Lbx 1 transcription factor X90829 1000-1306P-selectin (glycoprotein ligand-1) X91144 1095-1323Transcription factor SEF2 X91753 755-1054Macrophage mannose receptor Z11974 807-1197Rab-2 ras-related protein X95403 232-505Gluthathione S-transferase (theta X98055 14-298type1); phase II conjugation enzymeZyxin; LIM domain protein; alpha- X99063 1437-1812actinin binding proteinMet protooncogene Y00671 3646-3933c-Kit proto-oncogene (mast/stem cell Y00864 2867-3181growth factor receptor tyrosinekinase)Transcription factor BARX1 Y07960 723-973(homeodian transcription factor)PLC gamma; phospholipase C X95346 180-516gammaStromelysin-3: matrix Z12604 1463-1806metalloproteinase-11 (MMP-11)5-Hydroxytryptamine (serotonin) Z14224 530-774receptor 1e beta5-Hydroxytryptamine (serotonin) Z15119 588-940receptor 2cLow density lipoprotein receptor Z19521 1047-13245-Hydroxytryptamine (serotonin) Z23107 460-817receptor 7c-Mpl; thrombopoietin receptor; Z22649 1561-1772mematopoietic growth factor receptorsuperfamily memberDNA-polymerase delta catalytic Z21848 1256-1600subunitFollistatin Z29532 764-1053Cyclin F (S/G2/M-specific) Z47766 2431-2708Ets-related protein Sap 1A Z26885 1267-1521Net; ets related transcription factor; Z32815 1211-1595activated by RasStat5a; mammary gland factor Z48538 2269-2628Hek2 murine homologue; Mdk5 Z49086 1702-1930mouse developmental kinase; Eph -related tyrosine-protein kinasereceptorD-Factor/LIF receptor D26177 2376-2775Cytoskeletal epidermal keratin (14 M13806 108-469human)R-ras protein, closely related to ras M21019 215-555proto-oncogenesProlactin receptor PRLR2 M22959 1-328Blk; B lymphocyte kinase; Src M30903 1307-1672family memberMacrophage inflammatory protein 1 M35590 119-445beta (Act 2)Alpha-1 protease inhibitor 2 M75716 625-969GABA-A transporter 1Bone morphogenetic protein 8a M97017 788-1139(BMP-8a)(TGF-beta family)Erythroid kruppel-like transcription M97200 783-1171factorGATA binding transcription factor M98339 81-379(GATA-4)Growth factor receptor M98547 1701-2014Crk adaptor protein S72408 750-1027Retinoid X receptor interacting U09419 1388-1682protein (RIP 15)Cek 7 receptor protein tyrosine U14752 504-837kinase ligandC-C CKR-1; CCR-1; C-C chemokine U29678 168-495receptor type 1, macrophageinflammatory protein-1 alphareceptor; MIP-1alpha-R; RANTES-RGlucocorticoid receptor form A X13358 1527-1816Mothers against DPP protein (mad X83106 464-728homolog Smad 1, transforminggrowth factor beta signaling protein)Hck tyrosine-protein kinase Y00487 1308-1563Photolysase/blue-light receptor AB000777 1418-1737homologueOsp94 osmotic stress protein; APG- D49482 1026-12661; hsp70-relatedGlucose regulated protein, 78kD; D78645 167-411Grp78LCR-1; CXCR-4; CXC(SDF-1) D87747 584-867chemokine receptor 4; HIVcoreceptor (fusin); G protein-coupledreceptor LCR1 homologue;Glucose transporter-1, erythrocyte; M23384 325-653Glut1Int-3 proto-oncogene; NOTCH M80456 1846-2145family member; NOTCH4c-Akt proto-oncogene; Rac-alpha; M94335 604-899proteine kinase B (PKB)Bak apoptosis regulator; Bcl-2 Y13231 1509-1786family memberPS-2; homologue of the Alzheimer's U57324 437-783disease geneBRCA2; Breast cancer susceptibility U65594 649-922locus 2 productDNA ligase III U66058 2980-3205Caspase-7; Lice2; ICE-LAP3 U67321 1040-1280cysteine proteaseBID; apoptic death agonist U75506 452-777WBP6; pSK-SRPK1; WW domain U92456 482-774binding protein 6 serine kinase forSR splicing factorsCyclin G2 (G2/M-specific) U95826 408-688Ung1; uracil-DNA glycosylase X99018 444-729Rab-3b ras related protein Y14019 232-562Inhibitor of the RNA-activated U28423 180-487protein kinase, 58-kDaGolgi 4-transmembrane spanning U34259 742-1060transporter; MTPATP-binding casette 8; ABC8; U34920 1011-1319homolog of Drosophilia whiteCDC42 GTP-binding protein; G25K U37720 1675-1982Etoposide induced p53 responsive U41751 1041-1296(Et24) mRNACasein kinase II (alpha subunit) U51866 1237-1517TSG101 tumor susceptibility protein U52945 446-713Tumor suppressor maspin U54705 251-507FLIP-L, apoptosis inhibitor; FLICE- U97076 1476-1811like inhibitory proteinCamK II; Ca2+/calmodulin- X63615 1951-2219dependent protein kinase II (betasubunit)Htk; Mdk2 mouse developmental Z49085 2032-2365kinase; Eph-related tyrosine-proteinkinase receptorGlial cell line-derived neurotrophic D49921 236-539factorCD31 (Platelet endothelial cell L06039 1172-1494adhesion molecule 1)CD22 antigen L16928 2314-2645Gbx 2 L39970 1122-1395Cytotoxic T lymphocyte-specific M12302 585-830serine protease CCP I gene (CTLA-1)Cathepsin B M14222 384-729Growth hormone receptor M33324 1924-2240CD28 (receptor for B71) M34563 544-774Estrogen receptor M38651 742-1013Monotype chemoattractant protein 3 S71251 201-491CD45 associated protein (CD 45-ap, U03856 620-898LSM-1)Orphan receptor U11688 1686-1943Cannabinoid receptor 1 (brain) U17985 1091-1437Dystrogycan 1 U43512 2267-2505G-protein coupled receptor U46923 350-671Urokinase type plasminogen X02389 1301-1538activatorCTLA-4 (immunoglobin superfamily X05719 246-519member)Myogenic factor 5 X56182 232-528uPAR1; urokinase plasminogen X62700 482-756activator surface receptor (CD87)Serine protease inhibitor 2.4 X69832 621-927SRY-box containing gene 4 X70298 34-311Bone morphogenetic protein 2 L25602 8372-8724(BMP-2)(TGF-beta family)[K02588]P-1-450; dioxin-inducible M10021 3729-4014cytochrome P450 [K02588]Bcl-2; B cell lymphoma protein 2, M16506 2125-2367apoptosis inhibitorCD14 antigen M34510 667-931Somatostatin receptor 2 M81832 47-310Dopamine receptor 4 U19880 907-1191Cannabinoid receptor 2 U21681 910-1262(macrophage, CB2)Erf(Ets-related transcription factor) U58533 1286-16135-Hydroxytryptamine (serotonin) Z11597 1043-1355receptor 1bTob antoproliferative factor; interacts D78382 540-876with p185erbB2Gluthathione S-transferase J03752 185-428(microsomal)Adensine A3 receptor L20331 182-382p55cdc; cell division control protein U05341 1061-134820AP endonuclease; U12273 1894-2150apurinic/apyrimidinic endonuclease(Apex)Mas proto-oncogene (G-protein X67735 566-808coupled receptor)AT motif-binding factor ATBF1 D26046 9807-10112HMG-box transcription factor from D49474 427-662testis (MusSox17)Ikaros DNA binding protein L03547 627-890Early B cell factor (EBF) L12147 750-1026Engariled protein (En-1) homolog L12703 1323-1554Engrailed protein (En-2) homolog L12705 1626-1895Transcription factor A10 L21027 499-806Myocyte nuclear factor (MNF) L26507 1203-1456Basic domain/leucine zipper L36435 872-1073transcription factorCaudal type Homeobox 1 (Cdx1) M37163 1040-1301Butyrate response factor 1 M58566 768-22Brain specific transcription factor S53744 1548-1754NURR-1Brn-3.2 POU transcription factor S68377 877-1237Caudal type Homeobox 2 (Cdx2) S74520 1085-1367Erythroid transcription factor NF-E2 U01036 1-241Gut-specific Kruppel-like factor U20344 1558-1789GKLFKruppel-like factor LKLF U25096 898-1193Neuronal helix-loop-helix protein U29086 572-907NEX-1Brain factor 1 (Hfhbf1) U36760 1080-1318Split hand/foot gene U41626 92-303Sim transcription factor U42554 2828-3066Glial cells missing gene homolog U59876 727-1080(mGCM1)Sp4 zinc finger transcription factor U62522 1704-1929Heat shock transcription factor 2 X61754 1445-1640(HSF 2)RNA polymerase I termination factor X83974 3222-3433TTF-1Hepatocyte nuclear factor 3/forkhead L35949 913-1232homolog 8 (HFH-8)SRY-box containing gene 3 (Sox3) X94125 212-443Cot proto-oncogene D13759 696-956HR21spA; protein involved in DNA D49429 103-434double-strand break repair; PW29;calcium-binding proteinMmLim15; RecA-like gene; DMC1 D64107 581-781homologue; meiosis-specifichomologous recombination proteinERp72 endoplasmic reticulum stress J05186 1160-1470protein; protein disulfide isomerase-related proteinHMG1-related VDJ recombination S50213 2263-2531signal binding proteinGli oncogene; zinc finger S65038 104-505transcription factorTiam-1 invasion inducing protein; U05245 4329-4628GDP-GTP exchanger-relatedSik; Src-related intestinal kinase U16805 1246-1623Lfc proto-oncogene U28495 853-1150Oxidative stress-induced protein U40930 1248-1561mRNASTAM; signal transducing adaptor U43900 576-811moleculeShcC adaptor; Shc-related; brain- U46854 246-601specificMmMre11a putative U58987 866-1204endo/exonucleasePCNA; proliferating cell nuclear X53068 53-320antigen; processivity factorTranslin; recombination hotspot X81464 205-431binding proteinPA6 stromal protein; RAG1 gene X96618 442-749activatorSky proto-oncogene (Tyro3; Rse; U18342 1927-2286Dtk)H-ras proto-oncogene; transforming Z50013 1307-1544G-proteinERBB-2 receptor (c-neu; HER2 L47239 16-266protein tyrosine kinase)ERBB-3 receptor L47240 4-243Placental ribonuclease inhibitor U22516 512-766(Angiogenin)myosin I L00923 2578-2921Ca2+ binding protein, Cab45 U45977 597-1082murine ornithine decarboxylase M10624 865-1252______________________________________

It is evident from the above results and discussion that the subject invention provides a rapid, high throughput means to simply and quickly obtain a broad-scale screening of mouse gene expression in a variety of different samples. Only simple hybridization protocols need be employed with the subject arrays, and signals can be detected using any convenient and readily available detection device. Despite their simplicity, assays conducted with the subject arrays yield a large amount of information regarding the expression of numerous different and important key mouse genes. As such, the subject mouse arrays find use in a variety of different applications.

All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference. The citation of any publication is for its disclosure prior to the filing date and should not be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it is readily apparent to those of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims.

Claims

1. A mouse array comprising a plurality of polynucleotide probe spots stably associated with the surface of a solid support, wherein each polynucleotide probe spot comprises a polynucleotide probe composition made up of unique polynucleotides corresponding to a key mouse gene, wherein each of said unique polynucleotides: (a) does not cross-hybridize under stringent conditions with a polynucleotide of any other polynucleotide probe composition on the array; and (b) said unique polynucleotides of said array have an average length from about 120 to 700 nt.

2. The array according to claim 1, wherein said unique polynucleotides of said array have an average length of from about 200 to 600 nt.

3. The array according to claim 1, wherein said polynucleotide probe composition comprises a population of single stranded identical polynucleotides.

4. The array according to claim 1, wherein said polynucleotide probe composition comprises a population of two different complementary single stranded polynucleotides.

5. The array according to claim 1, wherein the density of spots on said array does not exceed about 400/cm.sup.2.

6. The array according to claim 1, wherein the number of polynucleotide probe spots on said array ranges from about 50 to 1000.

7. A mouse array comprising a plurality of 50 to 1000 polynucleotide probe spots stably associated with the surface of a solid support, wherein each polynucleotide probe spot comprises a polynucleotide probe composition made up of unique polynucleotides of from about 120 to 700 nt in length that do not cross-hybridize under stringent conditions with the polynucleotides of any other polynucleotide probe composition on the array and that correspond to a key mouse gene.

8. The array according to claim 7, wherein said polynucleotide probe composition comprises a population of single stranded identical polynucleotides.

9. The array according to claim 7, wherein said polynucleotide probe composition comprises a population of two different complementary single stranded polynucleotides.

10. The array according to claim 7, wherein the density of spots on said array does not exceed about 400/cm.sup.2.

11. The array according to claim 7, wherein at least 10 mouse genes of Table 1 are represented on said array.

12. A mouse array comprising from about 50 to 1000 polynucleotide probe spots stably associated with the surface of a solid support and having a density that does not exceed about 500 spots/cm.sup.2, wherein said plurality of polynucleotide probe spots comprises a polynucleotide probe composition made up of unique polynucleotides of from about 120 to 700 nt in average length that do not cross-hybridize under stringent conditions with the polynucleotides of any other polynucleotide probe composition on the array and all of the unique polynucleotides of said array correspond to key mouse genes, and further wherein at least 20 mouse genes listed in Table 1 are represented on said array.

13. The array according to claim 12, wherein each of said polynucleotide spots has a diameter ranging from about 10 to 5000 .mu.m.

14. A kit for use in a hybridization assay, said kit comprising:

a mouse array according to claim 1.

15. The kit according to claim 14, wherein said kit further comprises reagents for generating a labeled target polynucleotide sample.

16. The kit according to claim 14, wherein said kit further comprises a hybridization buffer.

17. The kit according to claim 14, wherein said kit further comprises a wash medium.