A 1 06-08-04_Hennighausen_Mouse430_2_KO1 GSP-EG001 Hennighausen A 2 06-08-04_Hennighausen_Mouse430_2_KO2 GSP-EG001 Hennighausen A 3 06-08-04_Hennighausen_Mouse430_2_KO3 GSP-EG001 Hennighausen A 4 06-08-04_Hennighausen_Mouse430_2_WT1 GSP-EG001 Hennighausen A 5 06-08-04_Hennighausen_Mouse430_2_WT2 GSP-EG001 Hennighausen A 6 06-08-04_Hennighausen_Mouse430_2_WT3 GSP-EG001 Hennighausen B 7 02-09-07_Hennighausen_PK_Mouse430_2_M42 GSP-EG003.1 Hennighausen B 8 02-09-07_Hennighausen_PK_Mouse430_2_M43 GSP-EG003.1 Hennighausen B 9 02-09-07_Hennighausen_PK_Mouse430_2_M44 GSP-EG003.1 Hennighausen B 10 02-09-07_Hennighausen_PK_Mouse430_2_M47 GSP-EG003.1 Hennighausen B 11 02-09-07_Hennighausen_PK_Mouse430_2_M48 GSP-EG003.1 Hennighausen B 12 02-09-07_Hennighausen_PK_Mouse430_2_M50 GSP-EG003.1 Hennighausen C 13 06-10-08_Hennighausen_1PK_Mouse430_2_4038WT GSP-EG003.2 Hennighausen C 14 06-10-08_Hennighausen_2PK_Mouse430_2_4060WT GSP-EG003.2 Hennighausen C 15 06-10-08_Hennighausen_3PK_Mouse430_2_4063WT GSP-EG003.2 Hennighausen C 16 06-10-08_Hennighausen_4PK_Mouse430_2_4035KO GSP-EG003.2 Hennighausen C 17 06-10-08_Hennighausen_5PK_Mouse430_2_4036KO GSP-EG003.2 Hennighausen C 18 06-10-08_Hennighausen_6PK_Mouse430_2_4042KO GSP-EG003.2 Hennighausen Gene Property Filtering 18 arrays and 45101 genes in the input dataset 18 arrays and 19 genes in the output dataset. 45082 genes excluded for Well ID not being in local list 'EG3-2-test-1-FC'. A A A A A A B B B B B B C C C C C C 06-08-04_Hennighausen_Mouse430_2_KO1 GSP-EG001 Hennighausen 06-08-04_Hennighausen_Mouse430_2_KO2 GSP-EG001 Hennighausen 06-08-04_Hennighausen_Mouse430_2_KO3 GSP-EG001 Hennighausen 06-08-04_Hennighausen_Mouse430_2_WT1 GSP-EG001 Hennighausen 06-08-04_Hennighausen_Mouse430_2_WT2 GSP-EG001 Hennighausen 06-08-04_Hennighausen_Mouse430_2_WT3 GSP-EG001 Hennighausen 02-09-07_Hennighausen_PK_Mouse430_2_M42 GSP-EG003.1 Hennighausen 02-09-07_Hennighausen_PK_Mouse430_2_M43 GSP-EG003.1 Hennighausen 02-09-07_Hennighausen_PK_Mouse430_2_M44 GSP-EG003.1 Hennighausen 02-09-07_Hennighausen_PK_Mouse430_2_M47 GSP-EG003.1 Hennighausen 02-09-07_Hennighausen_PK_Mouse430_2_M48 GSP-EG003.1 Hennighausen 02-09-07_Hennighausen_PK_Mouse430_2_M50 GSP-EG003.1 Hennighausen 06-10-08_Hennighausen_1PK_Mouse430_2_4038WT GSP-EG003.2 Hennighausen 06-10-08_Hennighausen_2PK_Mouse430_2_4060WT GSP-EG003.2 Hennighausen 06-10-08_Hennighausen_3PK_Mouse430_2_4063WT GSP-EG003.2 Hennighausen 06-10-08_Hennighausen_4PK_Mouse430_2_4035KO GSP-EG003.2 Hennighausen 06-10-08_Hennighausen_5PK_Mouse430_2_4036KO GSP-EG003.2 Hennighausen 06-10-08_Hennighausen_6PK_Mouse430_2_4042KO GSP-EG003.2 Hennighausen Well ID Feature ID Map mgB37_Probe Chr:Start-Stop mgB37_Probe Cytoband mgB37_RefSeq Chr:Start-Stop mgB37_RefSeq Cytoband Annotation_Src UniGene RefSeq Refseqs_Hit geneIDS_Hit Entrez GeneID Locus Tag Gene Description BioCarta Pathways KEGG Pathways Gene Ontology Terms GO Tier2 Component GO Tier3 Component GO Tier2 Function GO Tier3 Function GO Tier2 Process GO Tier3 Process 1388.3992 1437.2428 1340.8979 940.1353 832.1860 980.8734 1763.3867 1666.5310 414.8919 423.1519 1757.0016 399.0408 1091.3115 612.3186 635.9214 1565.4321 2320.3607 1921.4254 1327963 1416273_at 12 56.0 cM chr12:112692639-112692973 12 F1 chr12:112683139-112693229 12 F1 RSQ Mm.255332 NM_009396 1 1 21928 Tnfaip2 tumor necrosis factor, alpha-induced protein 2 (Tnfaip2), mRNA. angiogenesis;; cell differentiation;; multicellular organismal development anatomical structure formation;; cellular process;; developmental process;; multicellular organismal process anatomical structure development;; anatomical structure formation involved in morphogenesis;; anatomical structure morphogenesis;; cellular developmental process;; multicellular organismal development 24.4466 27.1615 22.7613 28.6837 27.8133 24.6695 273.2035 303.9363 66.7361 63.3636 290.5736 59.8105 74.1940 72.3079 66.3027 182.2095 154.0949 160.2428 1327998 1416318_at 13 12.0 cM chr13:32934621-32937204 13 A3.2 chr13:32933960-32943054 13 A3.2 RSQ Mm.20144 NM_025429 1 1 66222 RP23-427P14.4 Serpinb1a serine (or cysteine) peptidase inhibitor, clade B, member 1a (Serpinb1a), mRNA. cytoplasm;; endopeptidase inhibitor activity;; regulation of protein catabolic process;; serine-type endopeptidase inhibitor activity cell;; cell part cell part;; intracellular;; intracellular part enzyme regulator activity enzyme inhibitor activity biological regulation;; metabolic process;; regulation of biological process catabolic process;; macromolecule metabolic process;; primary metabolic process;; regulation of biological process;; regulation of metabolic process 103.8266 101.6423 94.7859 125.5332 190.5004 104.6094 1898.0111 1970.2178 1179.6578 1179.6042 1988.1943 1133.8942 269.9078 781.6517 228.4423 2008.4111 1945.6615 2428.3396 1329660 1418370_at 14 10.0 cM chr14:32023339-32024836 14 B chr14:32021497-32024897 14 B RSQ Mm.439921 NM_009393 1 1 21924 Tnnc1 troponin C, cardiac/slow skeletal (Tnnc1), mRNA. Calcium signaling pathway;; Cardiac muscle contraction CLASS Environmental Information Processing; Signal Transduction; Calcium signaling pathway [PATH:mmu04020] Cellular Processes; Circulatory System; Cardiac muscle contraction [PATH:mmu04260] actin filament binding;; calcium ion binding;; regulation of ATPase activity;; regulation of muscle filament sliding speed binding ion binding;; protein binding biological regulation;; cellular process;; establishment of localization;; localization;; multicellular organismal process;; regulation of biological process actin filament-based process;; cellular localization;; establishment of localization;; establishment of localization in cell;; regulation of biological process;; regulation of biological quality;; regulation of cellular process;; regulation of localization;; regulation of molecular function;; regulation of multicellular organismal process;; system process;; transport 24.3381 26.8275 24.6193 29.1122 30.9426 25.2384 130.8503 132.6910 41.4607 36.8201 138.7248 37.5598 30.1154 38.2075 40.1069 111.3767 89.7235 88.2856 1330250 1419086_at 5 chr5:44370129-44370679 5 B3 chr5:44370098-44373001 5 B3 RSQ Mm.46053 NM_008009 1 1 14181 Fgfbp1 fibroblast growth factor binding protein 1 (Fgfbp1), mRNA. extracellular region;; growth factor binding;; membrane;; plasma membrane cell;; cell part;; extracellular region cell part;; membrane binding protein binding 49.3526 35.9402 26.3882 66.7695 76.2624 51.1329 395.8032 357.7575 158.0785 155.9323 342.2051 135.7749 178.8438 211.0753 231.5755 587.5316 395.1282 487.1988 1331506 1420884_at 9 chr9:53698088-53701597 9 A5.3 chr9:53698057-53701656 9 A5.3 RSQ Mm.29132 NM_025540 1 1 66402 Sln sarcolipin (Sln), mRNA. enzyme regulator activity;; integral to membrane;; membrane;; sarcoplasmic reticulum cell;; cell part;; organelle cell part;; intracellular;; intracellular organelle;; intracellular part;; membrane;; membrane part;; membrane-bounded organelle enzyme regulator activity 109.1165 94.0396 122.5535 114.1721 114.3106 107.1515 246.8676 247.9234 104.3040 91.4115 243.2141 99.3919 113.1034 81.5462 77.9860 162.8186 218.5802 179.4852 1332186 1421830_at 4 47.6 cM chr4:101139016-101139266 4 C6 chr4:101092363-101139600 4 C6 RSQ Mm.42040 NM_009647 2 2 11639 RP23-301M3.3 Ak3l1 adenylate kinase 3-like 1 (Ak3l1), nuclear gene encoding mitochondrial protein, mRNA. Metabolic pathways CLASS Metabolism; Nucleotide Metabolism; Purine metabolism [PATH:mmu00230];; Purine metabolism adenylate kinase activity;; ATP binding;; GTP binding;; kinase activity;; mitochondrion;; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;; nucleobase, nucleoside, nucleotide kinase activity;; nucleotide binding;; nucleotide kinase activity;; phosphotransferase activity, phosphate group as acceptor;; transferase activity cell;; cell part;; organelle cell part;; intracellular;; intracellular organelle;; intracellular part;; membrane-bounded organelle binding;; catalytic activity nucleoside binding;; nucleotide binding;; transferase activity cellular process;; metabolic process cellular metabolic process;; nitrogen compound metabolic process;; primary metabolic process 109.5733 74.7981 111.1564 140.1180 170.6508 133.3669 1016.4785 1042.1023 491.3976 518.2960 997.3018 473.5159 517.6892 585.7949 674.0960 1349.6060 1406.0643 1441.9590 1332719 1422558_at 10 43.0 cM chr10:79721002-79722530 10 C1 chr10:79720895-79723713 10 C1 RSQ Mm.7329 NM_010255 1 1 14431 Gamt guanidinoacetate methyltransferase (Gamt), mRNA. Arginine and proline metabolism;; Glycine, serine and threonine metabolism;; Metabolic pathways CLASS Metabolism; Amino Acid Metabolism; Glycine, serine and threonine metabolism [PATH:mmu00260] Metabolism; Amino Acid Metabolism; Arginine and proline metabolism [PATH:mmu00330] creatine biosynthetic process;; guanidinoacetate N-methyltransferase activity;; methyltransferase activity;; organ morphogenesis;; regulation of multicellular organism growth;; spermatogenesis;; transferase activity catalytic activity transferase activity biological regulation;; cellular process;; developmental process;; growth;; metabolic process;; multicellular organismal process;; regulation of biological process;; reproduction;; reproductive process anatomical structure development;; anatomical structure morphogenesis;; biosynthetic process;; cellular metabolic process;; gamete generation;; multicellular organism growth;; multicellular organismal development;; nitrogen compound metabolic process;; primary metabolic process;; regulation of biological process;; regulation of growth;; regulation of multicellular organismal process;; reproductive process;; sexual reproduction 89.6202 100.3193 119.3163 125.0710 118.8532 117.4835 3774.1063 3798.2257 2516.2359 2468.5727 3992.7806 2416.3270 1112.3910 1549.3411 1482.3400 3852.3579 2425.2815 2524.0403 1335990 1427201_at 14 chr14:31692621-31694325 14 B chr14:31692442-31694796 14 B RSQ Mm.220895 NM_181390 1 1 66175 Mustn1 musculoskeletal, embryonic nuclear protein 1 (Mustn1), mRNA. nucleus cell;; cell part;; organelle cell part;; intracellular;; intracellular organelle;; intracellular part;; membrane-bounded organelle 1940.5295 1857.2588 1995.7352 1046.5408 924.9715 1194.3566 3396.0841 3344.4747 607.3380 666.1293 3253.4297 620.1634 1937.2358 1153.9852 1051.9975 2594.0235 3370.5477 2549.9669 1347930 1438855_x_at 12 56.0 cM chr12:112692993-112693192 12 F1 IPA Tnfaip2 tumor necrosis factor, alpha-induced protein 2 16.5279 18.6388 18.3893 19.6150 27.5955 20.6975 895.3741 917.2365 676.7113 598.8186 927.1719 615.1178 98.3841 328.7075 154.5816 769.0408 813.4041 721.9121 1348252 1448554_s_at 14 20.0 cM chr14:55590223-55591731 14 C3 chr14:55589524-55613386 14 C3 RSQ Mm.457983 NM_080728 2 2 140781 Myh7 myosin, heavy polypeptide 7, cardiac muscle, beta (Myh7), mRNA. Cardiac muscle contraction;; Tight junction CLASS Cellular Processes; Cell Communication; Tight junction [PATH:mmu04530] Cellular Processes; Circulatory System; Cardiac muscle contraction [PATH:mmu04260] actin binding;; ATP binding;; calmodulin binding;; cytoplasm;; motor activity;; myofibril;; myosin complex;; nucleotide binding;; striated muscle contraction;; striated muscle thick filament cell;; cell part;; macromolecular complex;; organelle;; organelle part cell part;; intracellular;; intracellular organelle;; intracellular organelle part;; intracellular part;; non-membrane-bounded organelle;; organelle part;; protein complex binding;; catalytic activity hydrolase activity;; nucleoside binding;; nucleotide binding;; protein binding multicellular organismal process system process 605.4722 797.3774 241.9977 1044.7616 2713.7768 856.5815 60.0072 57.7634 126.2640 107.7231 56.7346 117.4833 35.0984 23.1433 29.4871 67.2878 68.1489 56.9569 1339138 1448680_at 12 51.0 cM chr12:105133323-105135281 12 E chr12:105133135-105143160 12 E RSQ Mm.439694 NM_009245 2 2 20702 Serpina1c serine (or cysteine) peptidase inhibitor, clade A, member 1C (Serpina1c), mRNA. endopeptidase inhibitor activity;; extracellular region;; protein amino acid N-linked glycosylation;; protein binding;; response to cytokine stimulus;; response to peptide hormone stimulus;; serine-type endopeptidase inhibitor activity extracellular region binding;; enzyme regulator activity enzyme inhibitor activity;; protein binding cellular process;; metabolic process;; response to stimulus biosynthetic process;; cellular metabolic process;; macromolecule metabolic process;; primary metabolic process;; response to chemical stimulus;; response to endogenous stimulus 111.0782 114.5469 89.8428 131.3188 125.2634 161.9665 1616.6321 1516.8238 1056.8315 1009.4378 1470.3815 982.6807 249.1013 748.7493 300.0638 1856.5197 1897.4333 2285.0254 1340138 1449997_at 3 F1 chr3:89892969-89896013 3 F1 UGA Mm.240839 59069 Tpm3 Tropomyosin 3, gamma, mRNA (cDNA clone MGC:36031 IMAGE:4502880) Cardiac muscle contraction;; Pathways in cancer;; Thyroid cancer CLASS Cellular Processes; Circulatory System; Cardiac muscle contraction [PATH:mmu04260] Human Diseases; Cancers; Pathways in cancer [PATH:mmu05200] Human Diseases; Cancers; Thyroid Cancer [PATH:mmu05216] actin binding;; cleavage furrow;; cortical cytoskeleton;; cytoplasm;; cytoskeleton;; filamentous actin;; growth cone;; neuron projection;; podosome cell;; cell part;; macromolecular complex;; organelle;; organelle part cell division site;; cell division site part;; cell part;; cell projection;; intracellular;; intracellular organelle;; intracellular organelle part;; intracellular part;; non-membrane-bounded organelle;; organelle part;; protein complex;; site of polarized growth binding protein binding 138.3914 144.3297 176.2277 148.0226 176.4317 142.9258 405.0296 451.2680 157.1633 164.0247 397.8170 167.1677 218.2075 134.3381 114.9569 315.7167 362.3709 375.1926 1348663 1450387_s_at 4 47.6 cM chr4:101139123-101139504 4 C6 chr4:101092363-101139600 4 C6 RSQ Mm.42040 NM_009647 2 2 11639 RP23-301M3.3 Ak3l1 adenylate kinase 3-like 1 (Ak3l1), nuclear gene encoding mitochondrial protein, mRNA. Metabolic pathways CLASS Metabolism; Nucleotide Metabolism; Purine metabolism [PATH:mmu00230];; Purine metabolism adenylate kinase activity;; ATP binding;; GTP binding;; kinase activity;; mitochondrion;; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;; nucleobase, nucleoside, nucleotide kinase activity;; nucleotide binding;; nucleotide kinase activity;; phosphotransferase activity, phosphate group as acceptor;; transferase activity cell;; cell part;; organelle cell part;; intracellular;; intracellular organelle;; intracellular part;; membrane-bounded organelle binding;; catalytic activity nucleoside binding;; nucleotide binding;; transferase activity cellular process;; metabolic process cellular metabolic process;; nitrogen compound metabolic process;; primary metabolic process 118.4341 88.0124 124.0556 150.9327 170.7027 88.0575 982.1189 1039.9147 567.6175 559.6030 1021.2107 564.2468 146.8151 436.8152 198.0208 1158.1453 1100.0280 1474.7292 1348770 1450813_a_at 1 60.0 cM chr1:137696087-137707566 1 E4 RSQ Mm.44379 NM_001112702 2 1 21952 Tnni1 troponin I, skeletal, slow 1 (Tnni1), transcript variant 2, mRNA. actin binding;; ventricular cardiac muscle morphogenesis binding protein binding developmental process;; multicellular organismal process anatomical structure development;; anatomical structure morphogenesis;; multicellular organismal development 296.0767 276.1814 341.6162 243.6939 311.9855 224.9269 2130.3466 1995.0602 718.2331 749.8354 1993.9678 693.5062 563.5964 511.8688 736.6675 1215.0369 1560.5489 1229.2415 1343080 1460700_at 11 60.5 cM chr11:100748149-100748711 11 D chr11:100748123-100800825 11 D RSQ Mm.249934 NM_011486 3 1 20848 RP23-279L23.5 Stat3 signal transducer and activator of transcription 3 (Stat3), transcript variant 3, mRNA. EGF Signaling Pathway;; Erk1/Erk2 Mapk Signaling pathway;; IL 6 signaling pathway;; IL22 Soluble Receptor Signaling Pathway;; PDGF Signaling Pathway;; Role of ERBB2 in Signal Transduction and Oncology;; Signaling of Hepatocyte Growth Factor Receptor;; Stat3 Signaling Pathway;; TPO Signaling Pathway Acute myeloid leukemia CLASS Environmental Information Processing; Signal Transduction; Jak-STAT signaling pathway [PATH:mmu04630] Cellular Processes; Endocrine System; Adipocytokine signaling pathway [PATH:mmu04920] Cellular Processes; Immune System; Chemokine signaling pathway [PATH:mmu04062] Human Diseases; Cancers; Pathways in cancer [PATH:mmu05200];; Adipocytokine signaling pathway;; Chemokine signaling pathway;; Jak-STAT signaling pathway;; Pancreatic cancer;; Pathways in cancer acute-phase response;; calcium ion binding;; cytokine-mediated signaling pathway;; cytoplasm;; DNA binding;; eating behavior;; eye photoreceptor cell differentiation;; glucose homeostasis;; JAK-STAT cascade involved in growth hormone signaling pathway;; nucleus;; plasma membrane;; positive regulation of transcription from RNA polymerase II promoter;; protein binding;; protein dimerization activity;; protein kinase binding;; regulation of multicellular organism growth;; regulation of transcription from RNA polymerase II promoter;; regulation of transcription, DNA-dependent;; sequence-specific DNA binding;; sexual reproduction;; signal transducer activity;; signal transduction;; temperature homeostasis;; transcription;; transcription activator activity;; transcription factor activity;; transcription from RNA polymerase II promoter cell;; cell part;; organelle cell part;; intracellular;; intracellular organelle;; intracellular part;; membrane;; membrane-bounded organelle binding;; molecular transducer activity;; transcription regulator activity ion binding;; nucleic acid binding;; protein binding;; signal transducer activity;; transcription activator activity;; transcription factor activity biological regulation;; cellular process;; developmental process;; growth;; metabolic process;; multicellular organismal process;; positive regulation of biological process;; regulation of biological process;; reproduction;; response to stimulus anatomical structure development;; anatomical structure morphogenesis;; behavior;; biosynthetic process;; cell communication;; cellular developmental process;; cellular metabolic process;; cellular response to stimulus;; macromolecule metabolic process;; multicellular organism growth;; multicellular organismal development;; nitrogen compound metabolic process;; positive regulation of biological process;; positive regulation of cellular process;; positive regulation of metabolic process;; primary metabolic process;; regulation of biological process;; regulation of biological quality;; regulation of cellular process;; regulation of growth;; regulation of metabolic process;; regulation of multicellular organismal process;; response to chemical stimulus;; response to endogenous stimulus;; response to external stimulus;; response to stress;; sexual reproduction;; temperature homeostasis 92.3235 97.2647 96.0092 77.5455 129.5897 78.3745 491.9852 522.7671 170.5748 171.2306 497.5964 166.8491 208.0928 181.2786 169.2994 576.1519 675.4474 1166.6011 1370826 1428420_a_at 12 chr12:112667670-112669350 12 F1 chr12:112655640-112669394 12 F1 RSQ Mm.248640 NM_028807 1 1 74190 1200009I06Rik RIKEN cDNA 1200009I06 gene (1200009I06Rik), mRNA. 192.8256 157.7290 163.7672 89.1949 82.7376 131.3366 484.8186 501.9665 137.2189 154.7326 493.2433 165.5505 210.8462 215.7630 218.0549 459.4518 757.4940 561.2626 1365310 1453119_at 2 chr2:19581695-19582189 2 A3 UGA Mm.470264 Transcribed locus 56.9843 51.1179 53.7367 62.7476 55.2265 55.1888 80.3621 93.2247 99.7970 79.2927 81.0504 93.5868 195.5695 138.2218 161.4077 393.0408 457.7161 322.8464 1367914 1457102_at 18 chr18:68501510-68501988 18 E2 UGA Mm.95774 Transcribed locus 36.6653 48.8734 37.2443 37.8986 37.5324 40.2838 68.5118 85.7406 23.0482 31.0767 86.4653 25.8177 31.6866 34.7647 32.0440 106.5041 232.3178 226.1078 1368821 1458115_at 8 chr8:64401070-64401578 8 B3.1 UGA Mm.440931 Transcribed locus