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Coexpression cluster:C4521: Difference between revisions

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|ontology_enrichment_disease=DOID:193!1.38e-11!29;DOID:120!1.85e-10!27;DOID:2394!5.11e-09!14;DOID:305!2.20e-07!106
|ontology_enrichment_disease=DOID:193!1.38e-11!29;DOID:120!1.85e-10!27;DOID:2394!5.11e-09!14;DOID:305!2.20e-07!106
|ontology_enrichment_uberon=UBERON:0003914!3.81e-19!118;UBERON:0000922!1.46e-14!612;UBERON:0004119!3.67e-14!169;UBERON:0000925!3.67e-14!169;UBERON:0006595!3.67e-14!169;UBERON:0004111!1.64e-13!241;UBERON:0002050!1.04e-12!605;UBERON:0005423!1.04e-12!605;UBERON:0004535!1.04e-12!110;UBERON:0000923!1.12e-12!604;UBERON:0005291!1.12e-12!604;UBERON:0006598!1.12e-12!604;UBERON:0002532!1.12e-12!604;UBERON:0001009!1.33e-12!113;UBERON:0000466!1.88e-12!126;UBERON:0000467!6.79e-12!625;UBERON:0002049!6.83e-12!79;UBERON:0007798!6.83e-12!79;UBERON:0000480!6.89e-12!626;UBERON:0000477!6.98e-12!286;UBERON:0000468!1.30e-11!659;UBERON:0001007!1.48e-11!155;UBERON:0001555!1.48e-11!155;UBERON:0007026!1.48e-11!155;UBERON:0000481!3.33e-11!347;UBERON:0000464!3.73e-11!104;UBERON:0003104!6.20e-11!238;UBERON:0009142!6.20e-11!238;UBERON:0001637!1.01e-10!42;UBERON:0003509!1.01e-10!42;UBERON:0004572!1.01e-10!42;UBERON:0001048!1.35e-10!168;UBERON:0000490!1.64e-10!138;UBERON:0000926!2.49e-10!448;UBERON:0004120!2.49e-10!448;UBERON:0006603!2.49e-10!448;UBERON:0004921!3.24e-10!129;UBERON:0004185!3.24e-10!129;UBERON:0005156!7.25e-10!59;UBERON:0000990!7.25e-10!59;UBERON:0006554!7.98e-10!44;UBERON:0004872!8.09e-10!84;UBERON:0000055!1.05e-09!69;UBERON:0001008!1.17e-09!45;UBERON:0003103!1.82e-09!69;UBERON:0001981!3.66e-09!60;UBERON:0007500!3.66e-09!60;UBERON:0004537!3.66e-09!60;UBERON:0006965!3.66e-09!60;UBERON:0002553!7.78e-09!70;UBERON:0005911!1.19e-08!82;UBERON:0003886!2.30e-08!63;UBERON:0000483!3.04e-08!309;UBERON:0000025!3.04e-08!194;UBERON:0000119!3.39e-08!312;UBERON:0000077!3.47e-08!130;UBERON:0004573!3.67e-08!33;UBERON:0004571!3.67e-08!33;UBERON:0003133!3.69e-08!48;UBERON:0003100!3.92e-08!41;UBERON:0004176!6.01e-08!22;UBERON:0000992!1.23e-07!13;UBERON:0002100!1.28e-07!216;UBERON:0000991!1.42e-07!21;UBERON:0009196!1.42e-07!21;UBERON:0009117!1.42e-07!21;UBERON:0005564!1.42e-07!21;UBERON:0005177!1.61e-07!107;UBERON:0003134!3.59e-07!37;UBERON:0000474!3.59e-07!37;UBERON:0000058!6.06e-07!26
|ontology_enrichment_uberon=UBERON:0003914!3.81e-19!118;UBERON:0000922!1.46e-14!612;UBERON:0004119!3.67e-14!169;UBERON:0000925!3.67e-14!169;UBERON:0006595!3.67e-14!169;UBERON:0004111!1.64e-13!241;UBERON:0002050!1.04e-12!605;UBERON:0005423!1.04e-12!605;UBERON:0004535!1.04e-12!110;UBERON:0000923!1.12e-12!604;UBERON:0005291!1.12e-12!604;UBERON:0006598!1.12e-12!604;UBERON:0002532!1.12e-12!604;UBERON:0001009!1.33e-12!113;UBERON:0000466!1.88e-12!126;UBERON:0000467!6.79e-12!625;UBERON:0002049!6.83e-12!79;UBERON:0007798!6.83e-12!79;UBERON:0000480!6.89e-12!626;UBERON:0000477!6.98e-12!286;UBERON:0000468!1.30e-11!659;UBERON:0001007!1.48e-11!155;UBERON:0001555!1.48e-11!155;UBERON:0007026!1.48e-11!155;UBERON:0000481!3.33e-11!347;UBERON:0000464!3.73e-11!104;UBERON:0003104!6.20e-11!238;UBERON:0009142!6.20e-11!238;UBERON:0001637!1.01e-10!42;UBERON:0003509!1.01e-10!42;UBERON:0004572!1.01e-10!42;UBERON:0001048!1.35e-10!168;UBERON:0000490!1.64e-10!138;UBERON:0000926!2.49e-10!448;UBERON:0004120!2.49e-10!448;UBERON:0006603!2.49e-10!448;UBERON:0004921!3.24e-10!129;UBERON:0004185!3.24e-10!129;UBERON:0005156!7.25e-10!59;UBERON:0000990!7.25e-10!59;UBERON:0006554!7.98e-10!44;UBERON:0004872!8.09e-10!84;UBERON:0000055!1.05e-09!69;UBERON:0001008!1.17e-09!45;UBERON:0003103!1.82e-09!69;UBERON:0001981!3.66e-09!60;UBERON:0007500!3.66e-09!60;UBERON:0004537!3.66e-09!60;UBERON:0006965!3.66e-09!60;UBERON:0002553!7.78e-09!70;UBERON:0005911!1.19e-08!82;UBERON:0003886!2.30e-08!63;UBERON:0000483!3.04e-08!309;UBERON:0000025!3.04e-08!194;UBERON:0000119!3.39e-08!312;UBERON:0000077!3.47e-08!130;UBERON:0004573!3.67e-08!33;UBERON:0004571!3.67e-08!33;UBERON:0003133!3.69e-08!48;UBERON:0003100!3.92e-08!41;UBERON:0004176!6.01e-08!22;UBERON:0000992!1.23e-07!13;UBERON:0002100!1.28e-07!216;UBERON:0000991!1.42e-07!21;UBERON:0009196!1.42e-07!21;UBERON:0009117!1.42e-07!21;UBERON:0005564!1.42e-07!21;UBERON:0005177!1.61e-07!107;UBERON:0003134!3.59e-07!37;UBERON:0000474!3.59e-07!37;UBERON:0000058!6.06e-07!26
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}}
}}

Revision as of 13:02, 5 September 2012


Full id: C4521_bile_mesenchymal_meningioma_alveolar_Wilms_Small_prostate



Phase1 CAGE Peaks

Hg19::chr5:76114847..76114867,+p1@F2RL1
Hg19::chr5:76114872..76114892,+p2@F2RL1
Hg19::chr5:76114932..76114943,+p4@F2RL1


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
epithelial tube3.81e-19118
embryo1.46e-14612
endoderm-derived structure3.67e-14169
endoderm3.67e-14169
presumptive endoderm3.67e-14169
anatomical conduit1.64e-13241
embryonic structure1.04e-12605
developing anatomical structure1.04e-12605
cardiovascular system1.04e-12110
germ layer1.12e-12604
embryonic tissue1.12e-12604
presumptive structure1.12e-12604
epiblast (generic)1.12e-12604
circulatory system1.33e-12113
immaterial anatomical entity1.88e-12126
anatomical system6.79e-12625
vasculature6.83e-1279
vascular system6.83e-1279
anatomical group6.89e-12626
anatomical cluster6.98e-12286
multi-cellular organism1.30e-11659
digestive system1.48e-11155
digestive tract1.48e-11155
primitive gut1.48e-11155
multi-tissue structure3.33e-11347
anatomical space3.73e-11104
mesenchyme6.20e-11238
entire embryonic mesenchyme6.20e-11238
artery1.01e-1042
arterial blood vessel1.01e-1042
arterial system1.01e-1042
primordium1.35e-10168
unilaminar epithelium1.64e-10138
mesoderm2.49e-10448
mesoderm-derived structure2.49e-10448
presumptive mesoderm2.49e-10448
subdivision of digestive tract3.24e-10129
endodermal part of digestive tract3.24e-10129
reproductive structure7.25e-1059
reproductive system7.25e-1059
urinary system structure7.98e-1044
splanchnic layer of lateral plate mesoderm8.09e-1084
vessel1.05e-0969
renal system1.17e-0945
compound organ1.82e-0969
blood vessel3.66e-0960
epithelial tube open at both ends3.66e-0960
blood vasculature3.66e-0960
vascular cord3.66e-0960
anatomical cavity7.78e-0970
endo-epithelium1.19e-0882
body cavity precursor2.30e-0863
epithelium3.04e-08309
tube3.04e-08194
cell layer3.39e-08312
mixed endoderm/mesoderm-derived structure3.47e-08130
systemic artery3.67e-0833
systemic arterial system3.67e-0833
reproductive organ3.69e-0848
female organism3.92e-0841
external genitalia6.01e-0822
female gonad1.23e-0713
trunk1.28e-07216
gonad1.42e-0721
indifferent external genitalia1.42e-0721
indifferent gonad1.42e-0721
gonad primordium1.42e-0721
trunk region element1.61e-07107
female reproductive organ3.59e-0737
female reproductive system3.59e-0737
duct6.06e-0726
Disease
Ontology termp-valuen
reproductive organ cancer1.38e-1129
female reproductive organ cancer1.85e-1027
ovarian cancer5.11e-0914
carcinoma2.20e-07106


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
CTCF#1066435.360256373075030.0064925092527670.0280984242437317
E2F1#186934.907389214879320.008460985347239390.0327256073135447
E2F6#187635.017155731697390.00791769806886330.032395066544465
EP300#203336.77394172622320.003216880500103790.0168194133942598
FOXA2#3170324.63046375266526.68983856509345e-050.00107588550954696
HDAC2#3066313.41562023662630.0004140761399857210.00392999799927015
NANOG#79923329.24477848101273.99627955670032e-050.000740275701706678
NR3C1#2908314.9730233311730.0002978331194675480.00309907274724233
NRF1#4899312.21027944771090.0005492172401020010.00472991666026329
STAT3#6774310.51946499715420.0008589184530415310.00644985507026204
TAF7#6879311.43306940492390.0006690181981945830.00545147784982789
TCF12#6938310.63446490218640.0008313523990202070.00631504932731627
TCF7L2#6934310.77017656313730.0008003181298398380.00616768190395092
ZNF263#1012738.221841637010680.001799043925565870.010994812367147



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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