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Coexpression cluster:C2696: Difference between revisions

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|full_id=C2696_Alveolar_Amniotic_Mesenchymal_Mallassezderived_Placental_Adipocyte_Urothelial
|full_id=C2696_Alveolar_Amniotic_Mesenchymal_Mallassezderived_Placental_Adipocyte_Urothelial
|id=C2696
|id=C2696
|ontology_enrichment_celltype=CL:0000220!7.80e-30!246;CL:0002321!9.35e-30!248;CL:0000222!3.75e-24!119;CL:0000055!1.66e-23!180;CL:0000548!3.76e-23!679;CL:0000004!3.76e-23!679;CL:0000255!3.76e-23!679;CL:0000144!1.49e-22!625;CL:0000012!2.41e-22!682;CL:0002371!7.12e-21!591;CL:0000066!1.95e-14!254;CL:0000183!5.63e-13!59;CL:0000057!6.47e-13!75;CL:0000680!6.18e-12!57;CL:0000056!6.18e-12!57;CL:0000355!6.18e-12!57;CL:0000213!8.63e-12!57;CL:0000215!8.63e-12!57;CL:0002078!5.46e-11!44;CL:0000187!8.05e-11!54;CL:0000115!1.79e-10!35;CL:0000393!2.67e-10!60;CL:0000211!2.67e-10!60;CL:0000003!8.35e-10!722;CL:0000192!1.65e-09!42;CL:0000514!1.65e-09!42;CL:0002139!9.72e-09!24;CL:0000071!1.69e-07!18;CL:0002546!1.69e-07!18;CL:0000359!3.67e-07!32;CL:1000449!8.53e-07!16;CL:0002334!8.98e-07!12
|ontology_enrichment_celltype=CL:0002321!1.86e-30!250;CL:0000222!1.06e-24!121;CL:0000548!8.50e-22!679;CL:0000255!8.50e-22!679;CL:0002371!6.72e-20!588;CL:0000066!4.62e-14!253;CL:0000057!5.06e-13!76;CL:0000213!2.35e-12!58;CL:0000215!2.35e-12!58;CL:0000183!2.58e-12!59;CL:0000680!8.39e-12!58;CL:0000056!8.39e-12!58;CL:0000355!8.39e-12!58;CL:0002078!1.80e-11!45;CL:0000115!5.33e-11!36;CL:0000187!1.08e-10!55;CL:0000055!1.61e-10!106;CL:0000393!2.55e-10!61;CL:0000211!2.55e-10!61;CL:0000192!1.80e-09!43;CL:0000514!1.80e-09!43;CL:0000003!2.23e-09!722;CL:0002139!7.98e-09!24;CL:0000071!1.23e-07!18;CL:0002546!1.23e-07!18;CL:0000359!7.08e-07!32;CL:0002334!7.75e-07!12
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!4.22e-19!659;UBERON:0002049!4.33e-18!79;UBERON:0007798!4.33e-18!79;UBERON:0002100!4.96e-18!216;UBERON:0005256!2.73e-16!143;UBERON:0000467!5.92e-16!625;UBERON:0000480!9.02e-16!626;UBERON:0003914!1.41e-14!118;UBERON:0000055!1.67e-14!69;UBERON:0000926!6.29e-14!448;UBERON:0004120!6.29e-14!448;UBERON:0006603!6.29e-14!448;UBERON:0000486!7.35e-14!82;UBERON:0004872!1.58e-13!84;UBERON:0000914!1.94e-13!83;UBERON:0002329!1.94e-13!83;UBERON:0003077!1.94e-13!83;UBERON:0003059!1.94e-13!83;UBERON:0007282!1.94e-13!83;UBERON:0009618!1.94e-13!83;UBERON:0007285!1.94e-13!83;UBERON:0000490!1.95e-13!138;UBERON:0003104!4.11e-13!238;UBERON:0009142!4.11e-13!238;UBERON:0001981!9.01e-13!60;UBERON:0007500!9.01e-13!60;UBERON:0004537!9.01e-13!60;UBERON:0006965!9.01e-13!60;UBERON:0000922!1.02e-11!612;UBERON:0002050!2.88e-11!605;UBERON:0005423!2.88e-11!605;UBERON:0000923!3.52e-11!604;UBERON:0005291!3.52e-11!604;UBERON:0006598!3.52e-11!604;UBERON:0002532!3.52e-11!604;UBERON:0004535!3.58e-11!110;UBERON:0004290!4.64e-11!70;UBERON:0000475!1.07e-10!365;UBERON:0001009!1.94e-10!113;UBERON:0001134!1.94e-10!61;UBERON:0002036!1.94e-10!61;UBERON:0003082!1.94e-10!61;UBERON:0001637!2.65e-10!42;UBERON:0003509!2.65e-10!42;UBERON:0004572!2.65e-10!42;UBERON:0002385!2.91e-10!63;UBERON:0001015!2.91e-10!63;UBERON:0000383!2.91e-10!63;UBERON:0000481!5.53e-09!347;UBERON:0000119!6.75e-09!312;UBERON:0009569!7.12e-09!113;UBERON:0000483!9.51e-09!309;UBERON:0000487!5.11e-08!22;UBERON:0004573!5.50e-08!33;UBERON:0004571!5.50e-08!33;UBERON:0006914!1.17e-07!25;UBERON:0001986!1.69e-07!18;UBERON:0004638!1.69e-07!18;UBERON:0004852!1.69e-07!18;UBERON:0004211!8.53e-07!16;UBERON:0001285!8.53e-07!16;UBERON:0007684!8.53e-07!16;UBERON:0003220!8.53e-07!16;UBERON:0004208!8.53e-07!16
|ontology_enrichment_uberon=UBERON:0000468!8.15e-18!656;UBERON:0000475!2.68e-17!264;UBERON:0002049!3.02e-17!78;UBERON:0007798!3.02e-17!78;UBERON:0000467!7.34e-16!624;UBERON:0000480!1.12e-15!625;UBERON:0002100!3.84e-15!199;UBERON:0003914!4.66e-14!117;UBERON:0000490!4.84e-14!148;UBERON:0007503!8.01e-14!78;UBERON:0000055!9.57e-14!68;UBERON:0000486!1.32e-13!83;UBERON:0003104!2.54e-13!160;UBERON:0009142!2.54e-13!160;UBERON:0004872!6.12e-13!83;UBERON:0007500!4.67e-12!59;UBERON:0001981!4.67e-12!59;UBERON:0004537!4.67e-12!59;UBERON:0006965!4.67e-12!59;UBERON:0005256!1.06e-11!122;UBERON:0002329!8.29e-11!71;UBERON:0003059!8.29e-11!71;UBERON:0007282!8.29e-11!71;UBERON:0004290!8.29e-11!71;UBERON:0009618!8.29e-11!71;UBERON:0004535!1.27e-10!109;UBERON:0007524!2.27e-10!73;UBERON:0001134!2.67e-10!62;UBERON:0002036!2.67e-10!62;UBERON:0003082!2.67e-10!62;UBERON:0003077!2.90e-10!72;UBERON:0007285!2.90e-10!72;UBERON:0005423!3.29e-10!581;UBERON:0001637!4.18e-10!42;UBERON:0003509!4.18e-10!42;UBERON:0004572!4.18e-10!42;UBERON:0002385!4.23e-10!64;UBERON:0001015!4.23e-10!64;UBERON:0000383!4.23e-10!64;UBERON:0001009!6.55e-10!112;UBERON:0000922!8.98e-10!592;UBERON:0000477!4.11e-09!373;UBERON:0000119!7.87e-09!309;UBERON:0000483!1.08e-08!306;UBERON:0002050!1.71e-08!564;UBERON:0000926!2.13e-08!315;UBERON:0004120!2.13e-08!315;UBERON:0006603!2.13e-08!315;UBERON:0009569!2.45e-08!112;UBERON:0000487!4.01e-08!22;UBERON:0000481!7.94e-08!342;UBERON:0004573!9.73e-08!33;UBERON:0004571!9.73e-08!33;UBERON:0006914!1.07e-07!25;UBERON:0004638!1.23e-07!18;UBERON:0001986!1.23e-07!18;UBERON:0004852!1.23e-07!18;UBERON:0000923!1.32e-07!560;UBERON:0010316!1.32e-07!560;UBERON:0005291!1.32e-07!560;UBERON:0006598!1.32e-07!560;UBERON:0010317!1.32e-07!560;UBERON:0002532!1.32e-07!560;UBERON:0006554!4.94e-07!47
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513023140820569!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00818604792347129!CTCFL#140690;4:19.7464743589744:6.5732084880439e-06:0.000193271205316108!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199869569798754!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161147467818906!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434640136101357!ETS1#2113;4:9.72876092220234:0.000111595531741814:0.0015469771355964!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186383456847727!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248431217731189!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00307916304682601!JUNB#3726;4:30.6106326598211:1.13787152942193e-06:4.6621484763161e-05!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129670318812667!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000241932901241011!SP2#6668;4:26.1535304938446:2.13562021071447e-06:7.75259086502638e-05!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322770088154533!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.000970663076303722!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244647679167741!THAP1#55145;4:31.3691446028513:1.03171810326891e-06:4.32043331945877e-05!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106973318800191!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00347072094540007
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}}
}}

Revision as of 14:19, 19 October 2012


Full id: C2696_Alveolar_Amniotic_Mesenchymal_Mallassezderived_Placental_Adipocyte_Urothelial



Phase1 CAGE Peaks

Hg19::chr2:24307635..24307660,-p1@TP53I3
Hg19::chr2:24307664..24307682,-p6@TP53I3
Hg19::chr2:24307692..24307711,-p3@TP53I3
Hg19::chr2:24307712..24307742,-p2@TP53I3


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>

Cell Type
Ontology termp-valuen
embryonic cell1.86e-30250
mesodermal cell1.06e-24121
animal cell8.50e-22679
eukaryotic cell8.50e-22679
somatic cell6.72e-20588
epithelial cell4.62e-14253
fibroblast5.06e-1376
lining cell2.35e-1258
barrier cell2.35e-1258
contractile cell2.58e-1259
muscle precursor cell8.39e-1258
myoblast8.39e-1258
multi-potent skeletal muscle stem cell8.39e-1258
meso-epithelial cell1.80e-1145
endothelial cell5.33e-1136
muscle cell1.08e-1055
non-terminally differentiated cell1.61e-10106
electrically responsive cell2.55e-1061
electrically active cell2.55e-1061
smooth muscle cell1.80e-0943
smooth muscle myoblast1.80e-0943
native cell2.23e-09722
endothelial cell of vascular tree7.98e-0924
blood vessel endothelial cell1.23e-0718
embryonic blood vessel endothelial progenitor cell1.23e-0718
vascular associated smooth muscle cell7.08e-0732
preadipocyte7.75e-0712
Uber Anatomy
Ontology termp-valuen
multi-cellular organism8.15e-18656
organism subdivision2.68e-17264
vasculature3.02e-1778
vascular system3.02e-1778
anatomical system7.34e-16624
anatomical group1.12e-15625
trunk3.84e-15199
epithelial tube4.66e-14117
unilaminar epithelium4.84e-14148
epithelial vesicle8.01e-1478
vessel9.57e-1468
multilaminar epithelium1.32e-1383
mesenchyme2.54e-13160
entire embryonic mesenchyme2.54e-13160
splanchnic layer of lateral plate mesoderm6.12e-1383
epithelial tube open at both ends4.67e-1259
blood vessel4.67e-1259
blood vasculature4.67e-1259
vascular cord4.67e-1259
trunk mesenchyme1.06e-11122
somite8.29e-1171
presomitic mesoderm8.29e-1171
presumptive segmental plate8.29e-1171
dermomyotome8.29e-1171
trunk paraxial mesoderm8.29e-1171
cardiovascular system1.27e-10109
dense mesenchyme tissue2.27e-1073
skeletal muscle tissue2.67e-1062
striated muscle tissue2.67e-1062
myotome2.67e-1062
paraxial mesoderm2.90e-1072
presumptive paraxial mesoderm2.90e-1072
developing anatomical structure3.29e-10581
artery4.18e-1042
arterial blood vessel4.18e-1042
arterial system4.18e-1042
muscle tissue4.23e-1064
musculature4.23e-1064
musculature of body4.23e-1064
circulatory system6.55e-10112
embryo8.98e-10592
anatomical cluster4.11e-09373
cell layer7.87e-09309
epithelium1.08e-08306
embryonic structure1.71e-08564
mesoderm2.13e-08315
mesoderm-derived structure2.13e-08315
presumptive mesoderm2.13e-08315
subdivision of trunk2.45e-08112
simple squamous epithelium4.01e-0822
multi-tissue structure7.94e-08342
systemic artery9.73e-0833
systemic arterial system9.73e-0833
squamous epithelium1.07e-0725
blood vessel endothelium1.23e-0718
endothelium1.23e-0718
cardiovascular system endothelium1.23e-0718
germ layer1.32e-07560
germ layer / neural crest1.32e-07560
embryonic tissue1.32e-07560
presumptive structure1.32e-07560
germ layer / neural crest derived structure1.32e-07560
epiblast (generic)1.32e-07560
urinary system structure4.94e-0747


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
CCNT2#90546.336201576962630.0006203100587215640.00513023140820569
CTCF#1066445.360256373075030.001211145381643620.00818604792347129
CTCFL#140690419.74647435897446.5732084880439e-060.000193271205316108
EBF1#187948.9064668465690.00015887907472010.00199869569798754
ELF1#199744.258097958807540.003041525565781240.0161147467818906
EP300#203346.77394172622320.0004748459821442640.00434640136101357
ETS1#211349.728760922202340.0001115955317418140.0015469771355964
HEY1#2346244.040111043105710.00375304636917980.0186383456847727
HMGN3#932448.178547723350590.0002234570284440470.00248431217731189
IRF1#365947.63716375356390.0002938853996185490.00307916304682601
JUNB#3726430.61063265982111.13787152942193e-064.6621484763161e-05
RAD21#5885410.35503389545638.6948481184721e-050.00129670318812667
SMARCB1#6598418.25271578115749.00423392720929e-060.000241932901241011
SP2#6668426.15353049384462.13562021071447e-067.75259086502638e-05
TAF1#687243.343046285745290.008005664898701650.0322770088154533
TAF7#6879411.43306940492395.85061525419808e-050.000970663076303722
TBP#690843.706770687096390.005296377814784350.0244647679167741
THAP1#55145431.36914460285131.03171810326891e-064.32043331945877e-05
YY1#752844.911170749853860.00171871838055440.0106973318800191
ZBTB7A#5134147.35190930787590.000342223540015990.00347072094540007



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.

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