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Coexpression cluster:C4521: Difference between revisions

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|full_id=C4521_bile_mesenchymal_meningioma_alveolar_Wilms_Small_prostate
|full_id=C4521_bile_mesenchymal_meningioma_alveolar_Wilms_Small_prostate
|id=C4521
|id=C4521
|ontology_enrichment_celltype=CL:0000066!8.34e-24!254;CL:0002321!7.54e-20!248;CL:0000220!4.03e-19!246;CL:0002076!2.68e-14!43;CL:0000223!3.17e-14!59;CL:0000359!1.21e-07!32;CL:0000192!4.56e-07!42;CL:0000514!4.56e-07!42;CL:0002368!7.72e-07!13;CL:0000393!8.63e-07!60;CL:0000211!8.63e-07!60
|ontology_enrichment_celltype=CL:0000066!3.18e-25!253;CL:0002321!2.36e-19!250;CL:0002076!7.94e-16!42;CL:0000223!1.38e-15!58;CL:0000359!1.88e-07!32;CL:0002368!3.63e-07!13;CL:0002251!3.89e-07!20
|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!1.54e-11!29;DOID:120!2.04e-10!27;DOID:2394!7.94e-09!14;DOID:305!8.69e-08!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!1.01e-18!117;UBERON:0000477!6.14e-16!373;UBERON:0004119!4.03e-14!160;UBERON:0000925!4.03e-14!160;UBERON:0006595!4.03e-14!160;UBERON:0000922!1.01e-12!592;UBERON:0004535!1.43e-12!109;UBERON:0001009!1.71e-12!112;UBERON:0004111!2.80e-12!240;UBERON:0000467!1.07e-11!624;UBERON:0000480!1.17e-11!625;UBERON:0002049!1.20e-11!78;UBERON:0007798!1.20e-11!78;UBERON:0001007!2.72e-11!145;UBERON:0001555!2.72e-11!145;UBERON:0007026!2.72e-11!145;UBERON:0005423!3.28e-11!581;UBERON:0006554!4.54e-11!47;UBERON:0000475!6.03e-11!264;UBERON:0000468!6.42e-11!656;UBERON:0001008!7.22e-11!48;UBERON:0000466!1.19e-10!117;UBERON:0001637!2.22e-10!42;UBERON:0003509!2.22e-10!42;UBERON:0004572!2.22e-10!42;UBERON:0004921!2.26e-10!118;UBERON:0005156!3.76e-10!59;UBERON:0000990!3.76e-10!59;UBERON:0003103!4.61e-10!68;UBERON:0004872!6.81e-10!83;UBERON:0000055!1.67e-09!68;UBERON:0001048!2.18e-09!160;UBERON:0000464!2.29e-09!95;UBERON:0000481!2.87e-09!342;UBERON:0005911!2.95e-09!82;UBERON:0007500!3.38e-09!59;UBERON:0001981!3.38e-09!59;UBERON:0004537!3.38e-09!59;UBERON:0006965!3.38e-09!59;UBERON:0002100!1.17e-08!199;UBERON:0005177!1.21e-08!101;UBERON:0003100!1.48e-08!41;UBERON:0003133!2.73e-08!48;UBERON:0000483!4.13e-08!306;UBERON:0000119!4.52e-08!309;UBERON:0004176!4.71e-08!22;UBERON:0000490!4.88e-08!148;UBERON:0002050!6.09e-08!564;UBERON:0004573!8.24e-08!33;UBERON:0004571!8.24e-08!33;UBERON:0000992!1.06e-07!13;UBERON:0000991!1.10e-07!21;UBERON:0009196!1.10e-07!21;UBERON:0009117!1.10e-07!21;UBERON:0005564!1.10e-07!21;UBERON:0000025!1.46e-07!192;UBERON:0003134!2.17e-07!37;UBERON:0000474!2.17e-07!37;UBERON:0003104!3.01e-07!160;UBERON:0009142!3.01e-07!160;UBERON:0000923!3.57e-07!560;UBERON:0010316!3.57e-07!560;UBERON:0005291!3.57e-07!560;UBERON:0006598!3.57e-07!560;UBERON:0010317!3.57e-07!560;UBERON:0002532!3.57e-07!560
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280984242437317!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327256073135447!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032395066544465!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168194133942598!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107588550954696!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392999799927015!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000740275701706678!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309907274724233!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00472991666026329!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00644985507026204!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00545147784982789!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631504932731627!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00616768190395092!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.010994812367147
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}}
}}

Revision as of 16:01, 19 October 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 tube1.01e-18117
anatomical cluster6.14e-16373
endoderm-derived structure4.03e-14160
endoderm4.03e-14160
presumptive endoderm4.03e-14160
embryo1.01e-12592
cardiovascular system1.43e-12109
circulatory system1.71e-12112
anatomical conduit2.80e-12240
anatomical system1.07e-11624
anatomical group1.17e-11625
vasculature1.20e-1178
vascular system1.20e-1178
digestive system2.72e-11145
digestive tract2.72e-11145
primitive gut2.72e-11145
developing anatomical structure3.28e-11581
urinary system structure4.54e-1147
organism subdivision6.03e-11264
multi-cellular organism6.42e-11656
renal system7.22e-1148
immaterial anatomical entity1.19e-10117
artery2.22e-1042
arterial blood vessel2.22e-1042
arterial system2.22e-1042
subdivision of digestive tract2.26e-10118
reproductive structure3.76e-1059
reproductive system3.76e-1059
compound organ4.61e-1068
splanchnic layer of lateral plate mesoderm6.81e-1083
vessel1.67e-0968
primordium2.18e-09160
anatomical space2.29e-0995
multi-tissue structure2.87e-09342
endo-epithelium2.95e-0982
epithelial tube open at both ends3.38e-0959
blood vessel3.38e-0959
blood vasculature3.38e-0959
vascular cord3.38e-0959
trunk1.17e-08199
trunk region element1.21e-08101
female organism1.48e-0841
reproductive organ2.73e-0848
epithelium4.13e-08306
cell layer4.52e-08309
external genitalia4.71e-0822
unilaminar epithelium4.88e-08148
embryonic structure6.09e-08564
systemic artery8.24e-0833
systemic arterial system8.24e-0833
female gonad1.06e-0713
gonad1.10e-0721
indifferent external genitalia1.10e-0721
indifferent gonad1.10e-0721
gonad primordium1.10e-0721
tube1.46e-07192
female reproductive organ2.17e-0737
female reproductive system2.17e-0737
mesenchyme3.01e-07160
entire embryonic mesenchyme3.01e-07160
germ layer3.57e-07560
germ layer / neural crest3.57e-07560
embryonic tissue3.57e-07560
presumptive structure3.57e-07560
germ layer / neural crest derived structure3.57e-07560
epiblast (generic)3.57e-07560
Disease
Ontology termp-valuen
reproductive organ cancer1.54e-1129
female reproductive organ cancer2.04e-1027
ovarian cancer7.94e-0914
carcinoma8.69e-08106


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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