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MCL coexpression mm9:813: Difference between revisions

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{{MCL_coexpression_mm9
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biogenesis;0.00181597261659763;244585,102774!GO:0005813;centrosome;0.00521245039954293;244585,102774!GO:0030031;cell projection biogenesis;0.00521245039954293;244585,102774!GO:0005815;microtubule organizing center;0.00521245039954293;244585,102774!GO:0021915;neural tube development;0.00521245039954293;244585,102774!GO:0007380;specification of segmental identity, head;0.00521245039954293;244585!GO:0031344;regulation of cell projection organization and biogenesis;0.00521245039954293;102774!GO:0007382;specification of segmental identity, maxillary segment;0.00521245039954293;244585!GO:0035287;head segmentation;0.00521245039954293;244585!GO:0022038;corpus callosum development;0.00521245039954293;244585!GO:0042305;specification of segmental identity, mandibular segment;0.00521245039954293;244585!GO:0030092;regulation of flagellum biogenesis;0.00521245039954293;102774!GO:0035289;posterior head segmentation;0.00521245039954293;244585!GO:0045724;positive regulation of flagellum biogenesis;0.00521245039954293;102774!GO:0001654;eye development;0.00703231761823199;244585,102774!GO:0021670;lateral ventricle development;0.00810714557875194;244585!GO:0060039;pericardium development;0.00810714557875194;244585!GO:0021591;ventricular system development;0.00810714557875194;244585!GO:0021988;olfactory lobe development;0.010943147442655;244585!GO:0021772;olfactory bulb development;0.010943147442655;244585!GO:0035085;cilium axoneme;0.012685969360038;244585!GO:0043584;nose development;0.012685969360038;244585!GO:0001895;retinal homeostasis;0.012685969360038;102774!GO:0007423;sensory organ development;0.0139499293895927;244585,102774!GO:0035058;sensory cilium biogenesis;0.0140258332338738;102774!GO:0046548;retinal rod cell development;0.0140258332338738;102774!GO:0048598;embryonic morphogenesis;0.0144545584929123;244585,102774!GO:0051130;positive regulation of cellular component organization and biogenesis;0.014584868654392;102774!GO:0007350;blastoderm segmentation;0.014584868654392;244585!GO:0009296;flagellum biogenesis;0.014584868654392;102774!GO:0043009;chordate embryonic development;0.0151035449562389;244585,102774!GO:0009792;embryonic development ending in birth or egg hatching;0.0151035449562389;244585,102774!GO:0043064;flagellum organization and biogenesis;0.0154666814034071;102774!GO:0021532;neural tube patterning;0.0166638556714407;244585!GO:0007379;segment specification;0.0166638556714407;244585!GO:0005932;basal body;0.0175089628525996;244585!GO:0032990;cell part morphogenesis;0.0175089628525996;244585,102774!GO:0048858;cell projection morphogenesis;0.0175089628525996;244585,102774!GO:0030030;cell projection organization and biogenesis;0.0175089628525996;244585,102774!GO:0045494;photoreceptor cell maintenance;0.0182210999226393;102774!GO:0015630;microtubule cytoskeleton;0.0190610103069554;244585,102774!GO:0008589;regulation of smoothened signaling pathway;0.0203342613919625;244585!GO:0035115;embryonic forelimb morphogenesis;0.0203342613919625;244585!GO:0044441;cilium part;0.0221700589639689;244585!GO:0035116;embryonic hindlimb morphogenesis;0.0221700589639689;244585!GO:0042462;eye photoreceptor cell development;0.0221700589639689;102774!GO:0035136;forelimb morphogenesis;0.0232450541616362;244585!GO:0001754;eye photoreceptor cell differentiation;0.0242748426948801;102774!GO:0042461;photoreceptor cell development;0.0252621924078737;102774!GO:0019216;regulation of lipid metabolic process;0.0276619525470583;102774!GO:0001889;liver development;0.0293571774882767;244585!GO:0046530;photoreceptor cell differentiation;0.0293571774882767;102774!GO:0005930;axoneme;0.0293571774882767;244585!GO:0035137;hindlimb morphogenesis;0.0293571774882767;244585!GO:0022037;metencephalon development;0.0293571774882767;244585!GO:0021549;cerebellum development;0.0293571774882767;244585!GO:0021537;telencephalon development;0.0293571774882767;244585!GO:0001894;tissue homeostasis;0.0305940695014491;102774!GO:0009790;embryonic development;0.0305940695014491;244585,102774!GO:0048871;multicellular organismal homeostasis;0.0305940695014491;102774!GO:0043232;intracellular non-membrane-bound organelle;0.0305940695014491;244585,54194,102774!GO:0043228;non-membrane-bound organelle;0.0305940695014491;244585,54194,102774!GO:0000902;cell morphogenesis;0.0308300686697638;244585,102774!GO:0032989;cellular structure morphogenesis;0.0308300686697638;244585,102774!GO:0007224;smoothened signaling pathway;0.031319052062797;244585!GO:0009887;organ morphogenesis;0.0348488304909991;244585,102774!GO:0007368;determination of left/right symmetry;0.0363176403676828;244585!GO:0044430;cytoskeletal part;0.0363176403676828;244585,102774!GO:0009799;determination of symmetry;0.0363176403676828;244585!GO:0009855;determination of bilateral symmetry;0.0363176403676828;244585!GO:0016358;dendrite development;0.0398764047791684;102774!GO:0009880;embryonic pattern specification;0.0403253145120023;244585!GO:0030902;hindbrain development;0.0405181487833023;244585!GO:0007286;spermatid development;0.0405181487833023;102774!GO:0035282;segmentation;0.0405181487833023;244585!GO:0001843;neural tube closure;0.0405181487833023;102774!GO:0048592;eye morphogenesis;0.0405181487833023;102774!GO:0048515;spermatid differentiation;0.0409232834134139;102774!GO:0014020;primary neural tube formation;0.0413179107994317;102774!GO:0031072;heat shock protein binding;0.0429758044872341;67035!GO:0007399;nervous system development;0.0429758044872341;244585,102774!GO:0008270;zinc ion binding;0.0434286716614663;81003,22718,54194!GO:0051128;regulation of cellular component organization and biogenesis;0.0465727875817791;102774!GO:0001841;neural tube formation;0.0465727875817791;102774!GO:0001839;neural plate morphogenesis;0.0468707672082345;102774!GO:0001840;neural plate development;0.0474454949779165;102774!GO:0001838;embryonic epithelial tube 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|gostat_on_MCL_coexpression=GO:0042384;cilium biogenesis;0.00181597261659763;244585,102774!GO:0005813;centrosome;0.00521245039954293;244585,102774!GO:0030031;cell projection biogenesis;0.00521245039954293;244585,102774!GO:0005815;microtubule organizing center;0.00521245039954293;244585,102774!GO:0021915;neural tube development;0.00521245039954293;244585,102774!GO:0007380;specification of segmental identity, head;0.00521245039954293;244585!GO:0031344;regulation of cell projection organization and biogenesis;0.00521245039954293;102774!GO:0007382;specification of segmental identity, maxillary segment;0.00521245039954293;244585!GO:0035287;head segmentation;0.00521245039954293;244585!GO:0022038;corpus callosum development;0.00521245039954293;244585!GO:0042305;specification of segmental identity, mandibular segment;0.00521245039954293;244585!GO:0030092;regulation of flagellum biogenesis;0.00521245039954293;102774!GO:0035289;posterior head segmentation;0.00521245039954293;244585!GO:0045724;positive regulation of flagellum biogenesis;0.00521245039954293;102774!GO:0001654;eye development;0.00703231761823199;244585,102774!GO:0021670;lateral ventricle development;0.00810714557875194;244585!GO:0060039;pericardium development;0.00810714557875194;244585!GO:0021591;ventricular system development;0.00810714557875194;244585!GO:0021988;olfactory lobe development;0.010943147442655;244585!GO:0021772;olfactory bulb development;0.010943147442655;244585!GO:0035085;cilium axoneme;0.012685969360038;244585!GO:0043584;nose development;0.012685969360038;244585!GO:0001895;retinal homeostasis;0.012685969360038;102774!GO:0007423;sensory organ development;0.0139499293895927;244585,102774!GO:0035058;sensory cilium biogenesis;0.0140258332338738;102774!GO:0046548;retinal rod cell development;0.0140258332338738;102774!GO:0048598;embryonic morphogenesis;0.0144545584929123;244585,102774!GO:0051130;positive regulation of cellular component organization and biogenesis;0.014584868654392;102774!GO:0007350;blastoderm segmentation;0.014584868654392;244585!GO:0009296;flagellum biogenesis;0.014584868654392;102774!GO:0043009;chordate embryonic development;0.0151035449562389;244585,102774!GO:0009792;embryonic development ending in birth or egg hatching;0.0151035449562389;244585,102774!GO:0043064;flagellum organization and biogenesis;0.0154666814034071;102774!GO:0021532;neural tube patterning;0.0166638556714407;244585!GO:0007379;segment specification;0.0166638556714407;244585!GO:0005932;basal body;0.0175089628525996;244585!GO:0032990;cell part morphogenesis;0.0175089628525996;244585,102774!GO:0048858;cell projection morphogenesis;0.0175089628525996;244585,102774!GO:0030030;cell projection organization and biogenesis;0.0175089628525996;244585,102774!GO:0045494;photoreceptor cell maintenance;0.0182210999226393;102774!GO:0015630;microtubule cytoskeleton;0.0190610103069554;244585,102774!GO:0008589;regulation of smoothened signaling pathway;0.0203342613919625;244585!GO:0035115;embryonic forelimb morphogenesis;0.0203342613919625;244585!GO:0044441;cilium part;0.0221700589639689;244585!GO:0035116;embryonic hindlimb morphogenesis;0.0221700589639689;244585!GO:0042462;eye photoreceptor cell development;0.0221700589639689;102774!GO:0035136;forelimb morphogenesis;0.0232450541616362;244585!GO:0001754;eye photoreceptor cell differentiation;0.0242748426948801;102774!GO:0042461;photoreceptor cell development;0.0252621924078737;102774!GO:0019216;regulation of lipid metabolic process;0.0276619525470583;102774!GO:0001889;liver development;0.0293571774882767;244585!GO:0046530;photoreceptor cell differentiation;0.0293571774882767;102774!GO:0005930;axoneme;0.0293571774882767;244585!GO:0035137;hindlimb morphogenesis;0.0293571774882767;244585!GO:0022037;metencephalon development;0.0293571774882767;244585!GO:0021549;cerebellum development;0.0293571774882767;244585!GO:0021537;telencephalon development;0.0293571774882767;244585!GO:0001894;tissue homeostasis;0.0305940695014491;102774!GO:0009790;embryonic development;0.0305940695014491;244585,102774!GO:0048871;multicellular organismal homeostasis;0.0305940695014491;102774!GO:0043232;intracellular non-membrane-bound organelle;0.0305940695014491;244585,54194,102774!GO:0043228;non-membrane-bound organelle;0.0305940695014491;244585,54194,102774!GO:0000902;cell morphogenesis;0.0308300686697638;244585,102774!GO:0032989;cellular structure morphogenesis;0.0308300686697638;244585,102774!GO:0007224;smoothened signaling pathway;0.031319052062797;244585!GO:0009887;organ morphogenesis;0.0348488304909991;244585,102774!GO:0007368;determination of left/right symmetry;0.0363176403676828;244585!GO:0044430;cytoskeletal part;0.0363176403676828;244585,102774!GO:0009799;determination of symmetry;0.0363176403676828;244585!GO:0009855;determination of bilateral symmetry;0.0363176403676828;244585!GO:0016358;dendrite development;0.0398764047791684;102774!GO:0009880;embryonic pattern specification;0.0403253145120023;244585!GO:0030902;hindbrain development;0.0405181487833023;244585!GO:0007286;spermatid development;0.0405181487833023;102774!GO:0035282;segmentation;0.0405181487833023;244585!GO:0001843;neural tube closure;0.0405181487833023;102774!GO:0048592;eye morphogenesis;0.0405181487833023;102774!GO:0048515;spermatid differentiation;0.0409232834134139;102774!GO:0014020;primary neural tube formation;0.0413179107994317;102774!GO:0031072;heat shock protein binding;0.0429758044872341;67035!GO:0007399;nervous system development;0.0429758044872341;244585,102774!GO:0008270;zinc ion binding;0.0434286716614663;81003,22718,54194!GO:0051128;regulation of cellular component organization and biogenesis;0.0465727875817791;102774!GO:0001841;neural tube formation;0.0465727875817791;102774!GO:0001839;neural plate morphogenesis;0.0468707672082345;102774!GO:0001840;neural plate development;0.0474454949779165;102774!GO:0001838;embryonic epithelial tube formation;0.0474454949779165;102774!GO:0051082;unfolded protein binding;0.0477227257535389;67035!GO:0030534;adult behavior;0.0496068184300374;102774!
}}

Latest revision as of 15:56, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:104968878..104968952,+p1@Trim23
Mm9::chr17:32487480..32487513,-p1@Akap8l
Mm9::chr3:151856767..151856795,-p5@Dnajb4
Mm9::chr3:154756157..154756204,-p@chr3:154756157..154756204
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Mm9::chr5:110352652..110352683,+p1@ENSMUST00000112544
Mm9::chr7:28516392..28516416,+p2@Zfp60
Mm9::chr7:48888915..48888973,+p1@Zfp788
Mm9::chr8:93837122..93837178,-p1@Rpgrip1l
Mm9::chr9:59201237..59201272,-p1@Bbs4


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0042384cilium biogenesis0.00181597261659763
GO:0005813centrosome0.00521245039954293
GO:0030031cell projection biogenesis0.00521245039954293
GO:0005815microtubule organizing center0.00521245039954293
GO:0021915neural tube development0.00521245039954293
GO:0007380specification of segmental identity, head0.00521245039954293
GO:0031344regulation of cell projection organization and biogenesis0.00521245039954293
GO:0007382specification of segmental identity, maxillary segment0.00521245039954293
GO:0035287head segmentation0.00521245039954293
GO:0022038corpus callosum development0.00521245039954293
GO:0042305specification of segmental identity, mandibular segment0.00521245039954293
GO:0030092regulation of flagellum biogenesis0.00521245039954293
GO:0035289posterior head segmentation0.00521245039954293
GO:0045724positive regulation of flagellum biogenesis0.00521245039954293
GO:0001654eye development0.00703231761823199
GO:0021670lateral ventricle development0.00810714557875194
GO:0060039pericardium development0.00810714557875194
GO:0021591ventricular system development0.00810714557875194
GO:0021988olfactory lobe development0.010943147442655
GO:0021772olfactory bulb development0.010943147442655
GO:0035085cilium axoneme0.012685969360038
GO:0043584nose development0.012685969360038
GO:0001895retinal homeostasis0.012685969360038
GO:0007423sensory organ development0.0139499293895927
GO:0035058sensory cilium biogenesis0.0140258332338738
GO:0046548retinal rod cell development0.0140258332338738
GO:0048598embryonic morphogenesis0.0144545584929123
GO:0051130positive regulation of cellular component organization and biogenesis0.014584868654392
GO:0007350blastoderm segmentation0.014584868654392
GO:0009296flagellum biogenesis0.014584868654392
GO:0043009chordate embryonic development0.0151035449562389
GO:0009792embryonic development ending in birth or egg hatching0.0151035449562389
GO:0043064flagellum organization and biogenesis0.0154666814034071
GO:0021532neural tube patterning0.0166638556714407
GO:0007379segment specification0.0166638556714407
GO:0005932basal body0.0175089628525996
GO:0032990cell part morphogenesis0.0175089628525996
GO:0048858cell projection morphogenesis0.0175089628525996
GO:0030030cell projection organization and biogenesis0.0175089628525996
GO:0045494photoreceptor cell maintenance0.0182210999226393
GO:0015630microtubule cytoskeleton0.0190610103069554
GO:0008589regulation of smoothened signaling pathway0.0203342613919625
GO:0035115embryonic forelimb morphogenesis0.0203342613919625
GO:0044441cilium part0.0221700589639689
GO:0035116embryonic hindlimb morphogenesis0.0221700589639689
GO:0042462eye photoreceptor cell development0.0221700589639689
GO:0035136forelimb morphogenesis0.0232450541616362
GO:0001754eye photoreceptor cell differentiation0.0242748426948801
GO:0042461photoreceptor cell development0.0252621924078737
GO:0019216regulation of lipid metabolic process0.0276619525470583
GO:0001889liver development0.0293571774882767
GO:0046530photoreceptor cell differentiation0.0293571774882767
GO:0005930axoneme0.0293571774882767
GO:0035137hindlimb morphogenesis0.0293571774882767
GO:0022037metencephalon development0.0293571774882767
GO:0021549cerebellum development0.0293571774882767
GO:0021537telencephalon development0.0293571774882767
GO:0001894tissue homeostasis0.0305940695014491
GO:0009790embryonic development0.0305940695014491
GO:0048871multicellular organismal homeostasis0.0305940695014491
GO:0043232intracellular non-membrane-bound organelle0.0305940695014491
GO:0043228non-membrane-bound organelle0.0305940695014491
GO:0000902cell morphogenesis0.0308300686697638
GO:0032989cellular structure morphogenesis0.0308300686697638
GO:0007224smoothened signaling pathway0.031319052062797
GO:0009887organ morphogenesis0.0348488304909991
GO:0007368determination of left/right symmetry0.0363176403676828
GO:0044430cytoskeletal part0.0363176403676828
GO:0009799determination of symmetry0.0363176403676828
GO:0009855determination of bilateral symmetry0.0363176403676828
GO:0016358dendrite development0.0398764047791684
GO:0009880embryonic pattern specification0.0403253145120023
GO:0030902hindbrain development0.0405181487833023
GO:0007286spermatid development0.0405181487833023
GO:0035282segmentation0.0405181487833023
GO:0001843neural tube closure0.0405181487833023
GO:0048592eye morphogenesis0.0405181487833023
GO:0048515spermatid differentiation0.0409232834134139
GO:0014020primary neural tube formation0.0413179107994317
GO:0031072heat shock protein binding0.0429758044872341
GO:0007399nervous system development0.0429758044872341
GO:0008270zinc ion binding0.0434286716614663
GO:0051128regulation of cellular component organization and biogenesis0.0465727875817791
GO:0001841neural tube formation0.0465727875817791
GO:0001839neural plate morphogenesis0.0468707672082345
GO:0001840neural plate development0.0474454949779165
GO:0001838embryonic epithelial tube formation0.0474454949779165
GO:0051082unfolded protein binding0.0477227257535389
GO:0030534adult behavior0.0496068184300374



Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.10.294637
MA0004.10.394951
MA0006.10.670874
MA0007.10.38073
MA0009.10.82278
MA0014.10.67203
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.11.28203
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.589612
MA0050.11.10321
MA0051.10.542972
MA0052.10.84317
MA0055.10.0882028
MA0056.10
MA0057.10.258928
MA0058.10.305206
MA0059.10.316585
MA0060.12.21405
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.513723
MA0074.11.22546
MA0076.11.40007
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.413524
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.980871
MA0113.11.36684
MA0114.10.19245
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.11.54167
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.77191
MA0146.10.0548413
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.21.7688
MA0035.20.482026
MA0039.20.618828
MA0138.20.630612
MA0002.20.145685
MA0137.20.287486
MA0104.20.157347
MA0047.20.533516
MA0112.20.442124
MA0065.20.44341
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.581988
MA0155.10.490492
MA0156.11.39718
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.176565
MA0163.10.0600297
MA0164.10.508398
MA0080.20.267388
MA0018.21.28741
MA0099.20.624421
MA0079.20.253208
MA0102.21.5442
MA0258.10.180934
MA0259.10.571417
MA0442.10
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