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Coexpression cluster:C2529: Difference between revisions

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|full_id=C2529_Mesenchymal_Corneal_Urothelial_Cardiac_salivary_Sebocyte_Esophageal
|full_id=C2529_Mesenchymal_Corneal_Urothelial_Cardiac_salivary_Sebocyte_Esophageal
|id=C2529
|id=C2529
|ontology_enrichment_celltype=CL:0000220!3.45e-37!246;CL:0002321!5.65e-37!248;CL:0000055!1.14e-31!180;CL:0000222!2.98e-25!119;CL:0000183!1.21e-18!59;CL:0000680!2.00e-17!57;CL:0000056!2.00e-17!57;CL:0000355!2.00e-17!57;CL:0000187!2.14e-16!54;CL:0000393!2.12e-14!60;CL:0000211!2.12e-14!60;CL:0000192!3.93e-14!42;CL:0000514!3.93e-14!42;CL:0000057!1.65e-13!75;CL:0000144!2.45e-13!625;CL:0000548!2.61e-13!679;CL:0000004!2.61e-13!679;CL:0000255!2.61e-13!679;CL:0000066!1.01e-12!254;CL:0000012!1.25e-12!682;CL:0002371!1.23e-11!591;CL:0000359!1.96e-11!32;CL:0000213!5.29e-09!57;CL:0000215!5.29e-09!57;CL:0000221!1.12e-07!71;CL:0000076!2.31e-07!62
|ontology_enrichment_celltype=CL:0002321!2.77e-37!250;CL:0000222!5.77e-26!121;CL:0000183!1.59e-18!59;CL:0000680!1.19e-17!58;CL:0000056!1.19e-17!58;CL:0000355!1.19e-17!58;CL:0000055!6.26e-17!106;CL:0000187!1.07e-16!55;CL:0000393!1.44e-14!61;CL:0000211!1.44e-14!61;CL:0000192!1.71e-14!43;CL:0000514!1.71e-14!43;CL:0000057!2.42e-14!76;CL:0000548!2.74e-13!679;CL:0000255!2.74e-13!679;CL:0002371!3.15e-12!588;CL:0000066!4.86e-12!253;CL:0000359!1.59e-11!32;CL:0000213!2.34e-09!58;CL:0000215!2.34e-09!58;CL:0000221!7.99e-08!72;CL:0000076!2.10e-07!63;CL:0002078!4.26e-07!45
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!4.90e-25!365;UBERON:0000119!5.42e-23!312;UBERON:0005256!1.10e-22!143;UBERON:0000483!1.41e-22!309;UBERON:0000486!9.39e-22!82;UBERON:0002100!2.14e-21!216;UBERON:0000481!4.08e-20!347;UBERON:0000914!2.13e-19!83;UBERON:0002329!2.13e-19!83;UBERON:0003077!2.13e-19!83;UBERON:0003059!2.13e-19!83;UBERON:0007282!2.13e-19!83;UBERON:0009618!2.13e-19!83;UBERON:0007285!2.13e-19!83;UBERON:0002049!7.41e-19!79;UBERON:0007798!7.41e-19!79;UBERON:0003104!4.73e-18!238;UBERON:0009142!4.73e-18!238;UBERON:0003914!1.45e-17!118;UBERON:0004290!1.62e-17!70;UBERON:0000490!7.28e-17!138;UBERON:0004872!9.03e-16!84;UBERON:0000055!1.71e-15!69;UBERON:0000468!1.84e-15!659;UBERON:0001134!2.32e-15!61;UBERON:0002036!2.32e-15!61;UBERON:0003082!2.32e-15!61;UBERON:0002385!1.96e-14!63;UBERON:0001015!1.96e-14!63;UBERON:0000383!1.96e-14!63;UBERON:0001981!3.14e-14!60;UBERON:0007500!3.14e-14!60;UBERON:0004537!3.14e-14!60;UBERON:0006965!3.14e-14!60;UBERON:0000477!5.10e-14!286;UBERON:0000480!7.52e-13!626;UBERON:0000467!8.30e-13!625;UBERON:0001637!8.56e-13!42;UBERON:0003509!8.56e-13!42;UBERON:0004572!8.56e-13!42;UBERON:0003102!1.17e-12!95;UBERON:0004535!1.31e-12!110;UBERON:0001009!9.24e-12!113;UBERON:0004111!9.63e-12!241;UBERON:0000922!1.45e-11!612;UBERON:0002050!1.89e-11!605;UBERON:0005423!1.89e-11!605;UBERON:0000923!2.03e-11!604;UBERON:0005291!2.03e-11!604;UBERON:0006598!2.03e-11!604;UBERON:0002532!2.03e-11!604;UBERON:0004573!1.77e-10!33;UBERON:0004571!1.77e-10!33;UBERON:0005085!3.16e-08!29;UBERON:0001048!5.49e-08!168;UBERON:0002199!8.23e-08!45;UBERON:0002416!8.23e-08!45;UBERON:0000025!9.62e-08!194;UBERON:0009569!4.12e-07!113;UBERON:0001444!5.13e-07!48;UBERON:0002097!9.50e-07!40
|ontology_enrichment_uberon=UBERON:0000475!7.44e-24!264;UBERON:0000486!3.69e-22!83;UBERON:0000119!7.19e-22!309;UBERON:0000483!1.66e-21!306;UBERON:0003104!1.96e-21!160;UBERON:0009142!1.96e-21!160;UBERON:0007503!5.08e-21!78;UBERON:0005256!5.36e-20!122;UBERON:0002100!4.15e-19!199;UBERON:0000490!5.31e-19!148;UBERON:0002049!1.27e-18!78;UBERON:0007798!1.27e-18!78;UBERON:0002329!9.69e-18!71;UBERON:0003059!9.69e-18!71;UBERON:0007282!9.69e-18!71;UBERON:0004290!9.69e-18!71;UBERON:0009618!9.69e-18!71;UBERON:0003914!2.04e-17!117;UBERON:0000481!2.48e-17!342;UBERON:0007524!2.71e-17!73;UBERON:0003077!3.40e-17!72;UBERON:0007285!3.40e-17!72;UBERON:0000477!2.82e-16!373;UBERON:0000468!9.43e-16!656;UBERON:0001134!1.18e-15!62;UBERON:0002036!1.18e-15!62;UBERON:0003082!1.18e-15!62;UBERON:0004872!2.34e-15!83;UBERON:0000055!4.87e-15!68;UBERON:0002385!9.06e-15!64;UBERON:0001015!9.06e-15!64;UBERON:0000383!9.06e-15!64;UBERON:0000467!2.79e-14!624;UBERON:0000480!2.82e-14!625;UBERON:0007500!8.67e-14!59;UBERON:0001981!8.67e-14!59;UBERON:0004537!8.67e-14!59;UBERON:0006965!8.67e-14!59;UBERON:0003102!1.07e-13!99;UBERON:0004535!1.06e-12!109;UBERON:0001637!1.11e-12!42;UBERON:0003509!1.11e-12!42;UBERON:0004572!1.11e-12!42;UBERON:0001009!7.11e-12!112;UBERON:0004111!2.73e-11!240;UBERON:0004573!1.95e-10!33;UBERON:0004571!1.95e-10!33;UBERON:0000922!1.72e-09!592;UBERON:0002199!9.92e-09!46;UBERON:0002416!9.92e-09!46;UBERON:0005423!1.00e-08!581;UBERON:0005085!4.99e-08!31;UBERON:0002050!7.05e-08!564;UBERON:0002097!1.27e-07!41;UBERON:0000923!1.68e-07!560;UBERON:0010316!1.68e-07!560;UBERON:0005291!1.68e-07!560;UBERON:0006598!1.68e-07!560;UBERON:0010317!1.68e-07!560;UBERON:0002532!1.68e-07!560;UBERON:0000025!2.01e-07!192;UBERON:0001048!2.22e-07!160
|tf_chipseq_enrich=FOS#2353;4:8.9979553088944:0.000152514771116863:0.00194915445186907!FOSL2#2355;4:16.9302006045617:1.2165416097647e-05:0.000303957868856975!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00107161602194722!FOXA2#3170;4:24.6304637526652:2.71504128667089e-06:9.44243080048687e-05!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.00072191696730798!GTF2B#2959;4:31.9438299343242:9.59435337635006e-07:4.08822795704865e-05!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186144469654162!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391795599288258!MAFK#7975;4:27.1007331378299:1.85228494563408e-06:6.855095231647e-05!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157098061486738!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322359423354861!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.000969431074937638!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244323499380858!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00346701758616063
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}}
}}

Revision as of 14:07, 19 October 2012


Full id: C2529_Mesenchymal_Corneal_Urothelial_Cardiac_salivary_Sebocyte_Esophageal



Phase1 CAGE Peaks

Hg19::chr1:154943142..154943157,-p3@SHC1
Hg19::chr1:154943181..154943192,-p4@SHC1
Hg19::chr1:154943212..154943230,-p1@SHC1
Hg19::chr1:154943232..154943245,-p5@SHC1


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


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

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>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
organism subdivision7.44e-24264
multilaminar epithelium3.69e-2283
cell layer7.19e-22309
epithelium1.66e-21306
mesenchyme1.96e-21160
entire embryonic mesenchyme1.96e-21160
epithelial vesicle5.08e-2178
trunk mesenchyme5.36e-20122
trunk4.15e-19199
unilaminar epithelium5.31e-19148
vasculature1.27e-1878
vascular system1.27e-1878
somite9.69e-1871
presomitic mesoderm9.69e-1871
presumptive segmental plate9.69e-1871
dermomyotome9.69e-1871
trunk paraxial mesoderm9.69e-1871
epithelial tube2.04e-17117
multi-tissue structure2.48e-17342
dense mesenchyme tissue2.71e-1773
paraxial mesoderm3.40e-1772
presumptive paraxial mesoderm3.40e-1772
anatomical cluster2.82e-16373
multi-cellular organism9.43e-16656
skeletal muscle tissue1.18e-1562
striated muscle tissue1.18e-1562
myotome1.18e-1562
splanchnic layer of lateral plate mesoderm2.34e-1583
vessel4.87e-1568
muscle tissue9.06e-1564
musculature9.06e-1564
musculature of body9.06e-1564
anatomical system2.79e-14624
anatomical group2.82e-14625
epithelial tube open at both ends8.67e-1459
blood vessel8.67e-1459
blood vasculature8.67e-1459
vascular cord8.67e-1459
surface structure1.07e-1399
cardiovascular system1.06e-12109
artery1.11e-1242
arterial blood vessel1.11e-1242
arterial system1.11e-1242
circulatory system7.11e-12112
anatomical conduit2.73e-11240
systemic artery1.95e-1033
systemic arterial system1.95e-1033
embryo1.72e-09592
integument9.92e-0946
integumental system9.92e-0946
developing anatomical structure1.00e-08581
ectodermal placode4.99e-0831
embryonic structure7.05e-08564
skin of body1.27e-0741
germ layer1.68e-07560
germ layer / neural crest1.68e-07560
embryonic tissue1.68e-07560
presumptive structure1.68e-07560
germ layer / neural crest derived structure1.68e-07560
epiblast (generic)1.68e-07560
tube2.01e-07192
primordium2.22e-07160


Overrepresented TFBS (DNA) motifs on this co-expression cluster<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)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOS#235348.99795530889440.0001525147711168630.00194915445186907
FOSL2#2355416.93020060456171.2165416097647e-050.000303957868856975
FOXA1#3169411.08141974938556.62943068949433e-050.00107161602194722
FOXA2#3170424.63046375266522.71504128667089e-069.44243080048687e-05
GATA2#2624412.7449317335543.78864877853583e-050.00072191696730798
GTF2B#2959431.94382993432429.59435337635006e-074.08822795704865e-05
HEY1#2346244.040111043105710.00375304636917980.0186144469654162
JUND#372746.994663941871030.000417684217818580.00391795599288258
MAFK#7975427.10073313782991.85228494563408e-066.855095231647e-05
REST#597849.650028716128020.0001152825614219170.00157098061486738
TAF1#687243.343046285745290.008005664898701650.0322359423354861
TAF7#6879411.43306940492395.85061525419808e-050.000969431074937638
TBP#690843.706770687096390.005296377814784350.0244323499380858
ZBTB7A#5134147.35190930787590.000342223540015990.00346701758616063



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.