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Coexpression cluster:C4606: Difference between revisions

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|full_id=C4606_mature_choriocarcinoma_Endothelial_pancreatic_CD14_aorta_endometrial
|full_id=C4606_mature_choriocarcinoma_Endothelial_pancreatic_CD14_aorta_endometrial
|id=C4606
|id=C4606
|ontology_enrichment_celltype=CL:0000115!1.92e-15!35;CL:0002078!3.13e-14!44;CL:0002139!4.27e-13!24;CL:0000071!9.54e-11!18;CL:0002546!9.54e-11!18;CL:0000557!3.46e-08!71;CL:0000213!5.24e-08!57;CL:0000215!5.24e-08!57;CL:1000497!8.21e-08!18;CL:0002518!8.21e-08!18;CL:0000839!5.98e-07!70;CL:0002009!6.36e-07!65;CL:1000449!7.54e-07!16;CL:1000413!8.60e-07!9
|ontology_enrichment_celltype=CL:0000115!4.08e-15!36;CL:0002078!3.84e-14!45;CL:0002139!3.85e-12!24;CL:0000071!3.97e-10!18;CL:0002546!3.97e-10!18;CL:1000497!1.15e-08!17;CL:0002518!1.15e-08!17;CL:0000557!2.00e-08!67;CL:0000213!8.10e-08!58;CL:0000215!8.10e-08!58;CL:0000325!9.03e-08!87;CL:1000449!1.23e-07!15;CL:0002009!3.98e-07!61;CL:0000839!4.27e-07!66
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000926!1.24e-13!448;UBERON:0004120!1.24e-13!448;UBERON:0006603!1.24e-13!448;UBERON:0003914!1.02e-12!118;UBERON:0003081!5.50e-12!216;UBERON:0001986!9.54e-11!18;UBERON:0004638!9.54e-11!18;UBERON:0004852!9.54e-11!18;UBERON:0000468!1.23e-10!659;UBERON:0002405!5.00e-10!115;UBERON:0000922!6.15e-10!612;UBERON:0000487!1.58e-09!22;UBERON:0000480!1.88e-09!626;UBERON:0000467!3.39e-09!625;UBERON:0002417!5.09e-09!61;UBERON:0000916!5.09e-09!61;UBERON:0002050!5.93e-09!605;UBERON:0005423!5.93e-09!605;UBERON:0000923!6.84e-09!604;UBERON:0005291!6.84e-09!604;UBERON:0006598!6.84e-09!604;UBERON:0002532!6.84e-09!604;UBERON:0005172!1.38e-08!55;UBERON:0005173!1.38e-08!55;UBERON:0000055!2.28e-08!69;UBERON:0000025!2.90e-08!194;UBERON:0006914!3.79e-08!25;UBERON:0004111!4.38e-08!241;UBERON:0002553!6.22e-08!70;UBERON:0000466!1.04e-07!126;UBERON:0009569!1.10e-07!113;UBERON:0003886!1.54e-07!63;UBERON:0003887!2.43e-07!21;UBERON:0000477!2.76e-07!286;UBERON:0005177!4.72e-07!107;UBERON:0006555!5.90e-07!17;UBERON:0005103!5.90e-07!17;UBERON:0000083!5.90e-07!17;UBERON:0009201!5.90e-07!17;UBERON:0004819!5.90e-07!17;UBERON:0006553!5.90e-07!17;UBERON:0003074!5.90e-07!17;UBERON:0003060!5.90e-07!17;UBERON:0002049!6.98e-07!79;UBERON:0007798!6.98e-07!79;UBERON:0000080!7.10e-07!18;UBERON:0002120!7.10e-07!18;UBERON:0004875!7.10e-07!18;UBERON:0005721!7.10e-07!18;UBERON:0005754!7.10e-07!18;UBERON:0007297!7.10e-07!18;UBERON:0004211!7.54e-07!16;UBERON:0001285!7.54e-07!16;UBERON:0007684!7.54e-07!16;UBERON:0003220!7.54e-07!16;UBERON:0004208!7.54e-07!16;UBERON:0001981!8.50e-07!60;UBERON:0007500!8.50e-07!60;UBERON:0004537!8.50e-07!60;UBERON:0006965!8.50e-07!60;UBERON:0002371!8.57e-07!80;UBERON:0003915!8.60e-07!9;UBERON:0004700!8.60e-07!9;UBERON:0001917!8.60e-07!9
|ontology_enrichment_uberon=UBERON:0003914!6.34e-13!117;UBERON:0004638!3.97e-10!18;UBERON:0001986!3.97e-10!18;UBERON:0004852!3.97e-10!18;UBERON:0000468!7.25e-10!656;UBERON:0002417!9.70e-10!60;UBERON:0000916!9.70e-10!60;UBERON:0000922!1.48e-09!592;UBERON:0003081!2.09e-09!203;UBERON:0005172!2.28e-09!54;UBERON:0005173!2.28e-09!54;UBERON:0000487!8.02e-09!22;UBERON:0000055!3.13e-08!68;UBERON:0000480!3.32e-08!625;UBERON:0005423!4.57e-08!581;UBERON:0009569!5.16e-08!112;UBERON:0002405!5.28e-08!93;UBERON:0000467!5.60e-08!624;UBERON:0005177!1.05e-07!101;UBERON:0000025!1.10e-07!192;UBERON:0006555!1.19e-07!16;UBERON:0004819!1.19e-07!16;UBERON:0004211!1.23e-07!15;UBERON:0009773!1.23e-07!15;UBERON:0001231!1.23e-07!15;UBERON:0001285!1.23e-07!15;UBERON:0007684!1.23e-07!15;UBERON:0004208!1.23e-07!15;UBERON:0004111!1.24e-07!240;UBERON:0006914!1.28e-07!25;UBERON:0000477!1.42e-07!373;UBERON:0002371!6.83e-07!76;UBERON:0007500!7.36e-07!59;UBERON:0001981!7.36e-07!59;UBERON:0004537!7.36e-07!59;UBERON:0006965!7.36e-07!59
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.019102117304232!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115728627002291!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324090326715271!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464692332168155!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168303668244835!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154760359584456!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109129974658523!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157580467037542!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000740669814768811!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270748398305223!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247776126351794!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00545360533884203!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631780638879949!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00616995830533276!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249326488508617!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618550980493066!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000648837824706582!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331061642674845!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140848561363501
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}}
}}

Revision as of 16:05, 19 October 2012


Full id: C4606_mature_choriocarcinoma_Endothelial_pancreatic_CD14_aorta_endometrial



Phase1 CAGE Peaks

Hg19::chr6:44187265..44187308,+p3@SLC29A1
Hg19::chr6:44187309..44187329,+p4@SLC29A1
Hg19::chr6:44187334..44187387,+p2@SLC29A1


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
epithelial tube6.34e-13117
blood vessel endothelium3.97e-1018
endothelium3.97e-1018
cardiovascular system endothelium3.97e-1018
multi-cellular organism7.25e-10656
abdominal segment of trunk9.70e-1060
abdomen9.70e-1060
embryo1.48e-09592
lateral plate mesoderm2.09e-09203
abdomen element2.28e-0954
abdominal segment element2.28e-0954
simple squamous epithelium8.02e-0922
vessel3.13e-0868
anatomical group3.32e-08625
developing anatomical structure4.57e-08581
subdivision of trunk5.16e-08112
immune system5.28e-0893
anatomical system5.60e-08624
trunk region element1.05e-07101
tube1.10e-07192
excretory tube1.19e-0716
kidney epithelium1.19e-0716
nephron epithelium1.23e-0715
renal tubule1.23e-0715
nephron tubule1.23e-0715
nephron1.23e-0715
uriniferous tubule1.23e-0715
nephrogenic mesenchyme1.23e-0715
anatomical conduit1.24e-07240
squamous epithelium1.28e-0725
anatomical cluster1.42e-07373
bone marrow6.83e-0776
epithelial tube open at both ends7.36e-0759
blood vessel7.36e-0759
blood vasculature7.36e-0759
vascular cord7.36e-0759


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#90536.336201576962630.003930750035764890.019102117304232
CEBPB#105137.971147625824820.001974187055288560.0115728627002291
E2F6#187635.017155731697390.00791769806886330.0324090326715271
ELF1#199734.258097958807540.01295179875054610.0464692332168155
EP300#203336.77394172622320.003216880500103790.0168303668244835
GABPB1#255337.067683836182170.002832212825417420.0154760359584456
HMGN3#932438.178547723350590.001827766942164210.0109129974658523
JUND#372736.994663941871030.002921845042734990.0157580467037542
NANOG#79923329.24477848101273.99627955670032e-050.000740669814768811
NFKB1#479035.488063424193840.006049381815655430.0270748398305223
SP1#666735.69838137814090.005403962701712170.0247776126351794
TAF7#6879311.43306940492390.0006690181981945830.00545360533884203
TCF12#6938310.63446490218640.0008313523990202070.00631780638879949
TCF7L2#6934310.77017656313730.0008003181298398380.00616995830533276
TFAP2A#7020316.5186343730450.0002218033880766340.00249326488508617
TFAP2C#7022310.80922860986020.0007916746575753130.00618550980493066
THAP1#55145331.36914460285133.23800758564397e-050.000648837824706582
YY1#752834.911170749853860.008441455341808260.0331061642674845
ZBTB7A#5134137.35190930787590.002516255860282270.0140848561363501



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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