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Coexpression cluster:C1334: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0005923!tight junction!0.00109318546569462!1366;92359$GO:0043296!apical junction complex!0.00109318546569462!1366;92359$GO:0016327!apicolateral plasma membrane!0.00109318546569462!1366;92359$GO:0005911!intercellular junction!0.00222815365861779!1366;92359$GO:0001892!embryonic placenta development!0.00546259906066675!6692$GO:0030054!cell junction!0.00907390042342841!1366;92359$GO:0044459!plasma membrane part!0.00956535539574324!6768;1366;92359$GO:0001890!placenta development!0.0127967491689525!6692$GO:0016338!calcium-independent cell-cell adhesion!0.0166780129869154!1366$GO:0001763!morphogenesis of a branching structure!0.0218233954500037!6692$GO:0005886!plasma membrane!0.0262091988801033!6768;1366;92359$GO:0019897!extrinsic to plasma membrane!0.0262091988801033!6768$GO:0001701!in utero embryonic development!0.0262091988801033!6692$GO:0016324!apical plasma membrane!0.0330721699696492!92359$GO:0045177!apical part of cell!0.0380048061144456!92359$GO:0009792!embryonic development ending in birth or egg hatching!0.0380048061144456!6692$GO:0043009!chordate embryonic development!0.0380048061144456!6692$GO:0019898!extrinsic to membrane!0.0404059085111664!6768
|gostat_on_coexpression_clusters=GO:0005923!tight junction!0.00109318546569462!1366;92359$GO:0043296!apical junction complex!0.00109318546569462!1366;92359$GO:0016327!apicolateral plasma membrane!0.00109318546569462!1366;92359$GO:0005911!intercellular junction!0.00222815365861779!1366;92359$GO:0001892!embryonic placenta development!0.00546259906066675!6692$GO:0030054!cell junction!0.00907390042342841!1366;92359$GO:0044459!plasma membrane part!0.00956535539574324!6768;1366;92359$GO:0001890!placenta development!0.0127967491689525!6692$GO:0016338!calcium-independent cell-cell adhesion!0.0166780129869154!1366$GO:0001763!morphogenesis of a branching structure!0.0218233954500037!6692$GO:0005886!plasma membrane!0.0262091988801033!6768;1366;92359$GO:0019897!extrinsic to plasma membrane!0.0262091988801033!6768$GO:0001701!in utero embryonic development!0.0262091988801033!6692$GO:0016324!apical plasma membrane!0.0330721699696492!92359$GO:0045177!apical part of cell!0.0380048061144456!92359$GO:0009792!embryonic development ending in birth or egg hatching!0.0380048061144456!6692$GO:0043009!chordate embryonic development!0.0380048061144456!6692$GO:0019898!extrinsic to membrane!0.0404059085111664!6768
|id=C1334
|id=C1334
|ontology_enrichment_celltype=CL:0000066!1.61e-26!254;CL:0002076!1.31e-14!43;CL:0000223!6.49e-14!59;CL:0002368!1.31e-07!13;CL:0002251!4.67e-07!21
|ontology_enrichment_celltype=CL:0000066!3.56e-30!253;CL:0002076!8.35e-21!42;CL:0000223!3.50e-18!58;CL:0002368!2.38e-10!13;CL:0002251!6.73e-10!20;CL:0002159!4.15e-08!14;CL:1000507!6.93e-08!10;CL:1000494!6.93e-08!10;CL:0002202!3.14e-07!9;CL:0002632!3.14e-07!9;CL:0000039!6.71e-07!7;CL:0000586!6.71e-07!7
|ontology_enrichment_disease=DOID:305!2.23e-21!106;DOID:0050687!2.03e-12!143;DOID:1749!2.37e-08!14;DOID:299!1.93e-07!25
|ontology_enrichment_disease=DOID:305!1.63e-17!106;DOID:1749!1.67e-10!14;DOID:0050687!1.73e-10!143;DOID:299!9.09e-08!25
|ontology_enrichment_uberon=UBERON:0004119!1.09e-19!169;UBERON:0000925!1.09e-19!169;UBERON:0006595!1.09e-19!169;UBERON:0001007!1.91e-15!155;UBERON:0001555!1.91e-15!155;UBERON:0007026!1.91e-15!155;UBERON:0004921!2.83e-15!129;UBERON:0004185!2.83e-15!129;UBERON:0000077!2.58e-13!130;UBERON:0001004!1.44e-12!72;UBERON:0000466!1.22e-10!126;UBERON:0001041!2.54e-10!98;UBERON:0000065!2.82e-10!53;UBERON:0000464!4.83e-10!104;UBERON:0005911!1.17e-09!82;UBERON:0008947!3.51e-08!38;UBERON:0003258!3.51e-08!38;UBERON:0000072!1.33e-07!46;UBERON:0000062!1.63e-07!511;UBERON:0005177!1.90e-07!107;UBERON:0005153!2.62e-07!37;UBERON:0001008!3.95e-07!45;UBERON:0006554!7.24e-07!44
|ontology_enrichment_uberon=UBERON:0004119!6.11e-25!160;UBERON:0000925!6.11e-25!160;UBERON:0006595!6.11e-25!160;UBERON:0001007!1.92e-19!145;UBERON:0001555!1.92e-19!145;UBERON:0007026!1.92e-19!145;UBERON:0004921!2.22e-18!118;UBERON:0001004!1.11e-12!74;UBERON:0000464!1.44e-12!95;UBERON:0000466!2.01e-12!117;UBERON:0005911!5.67e-12!82;UBERON:0001041!2.29e-11!87;UBERON:0001008!2.70e-11!48;UBERON:0005177!3.00e-11!101;UBERON:0006554!7.70e-11!47;UBERON:0005153!1.15e-09!37;UBERON:0000065!5.16e-09!54;UBERON:0000161!5.87e-09!36;UBERON:0000062!2.59e-08!503;UBERON:0005178!2.61e-08!34;UBERON:0002224!2.61e-08!34;UBERON:0005156!2.85e-08!59;UBERON:0000990!2.85e-08!59;UBERON:0009569!3.35e-08!112;UBERON:0004810!6.93e-08!10;UBERON:0005181!7.17e-08!35;UBERON:0005157!9.77e-08!47;UBERON:0003101!3.03e-07!22;UBERON:0000079!3.03e-07!22;UBERON:0000475!3.57e-07!264;UBERON:0003133!5.88e-07!48
|pathway_enrichment=0.000128481434866115;0.0406643741351255;2;133;Tight junction (KEGG):04530!6.82636944046713e-05;0.0406643741351255;2;97;Cell junction organization (Reactome):REACT_20676
|pathway_enrichment=0.000128481434866115;0.0406643741351255;2;133;Tight junction (KEGG):04530!6.82636944046713e-05;0.0406643741351255;2;97;Cell junction organization (Reactome):REACT_20676
|tf_chipseq_enrich=E2F1#1869;5:4.08949101239944:0.00174981759776199:0.0107556471127458!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0379943416528497!SUZ12#23512;2:16.7052603036876:0.00566023468207957:0.0255576848232472!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.00572641546209186!ZEB1#6935;6:16.8884320175439:4.30431371220266e-08:2.827284401187e-06
|tf_chipseq_enrich=E2F1#1869;5:4.08949101239944:0.00174981759776199:0.0107556471127458!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0379943416528497!SUZ12#23512;2:16.7052603036876:0.00566023468207957:0.0255576848232472!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.00572641546209186!ZEB1#6935;6:16.8884320175439:4.30431371220266e-08:2.827284401187e-06
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}}
}}

Revision as of 11:09, 19 October 2012


Full id: C1334_Alveolar_gall_Renal_nasal_Prostate_signet_colon



Phase1 CAGE Peaks

Hg19::chr11:130029635..130029654,+p3@ST14
Hg19::chr11:130029668..130029690,+p1@ST14
Hg19::chr15:41136360..41136365,+p8@SPINT1
Hg19::chr15:41136369..41136420,+p3@SPINT1
Hg19::chr17:7165787..7165807,-p1@CLDN7
Hg19::chr19:6464243..6464325,+p1@CRB3


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


p.valueFDRnGenesnPathwayName
0.0001284814348661150.04066437413512552133Tight junction (KEGG):04530
6.82636944046713e-050.0406643741351255297Cell junction organization (Reactome):REACT_20676



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


GO IDGO nameFDR corrected p-value
GO:0005923tight junction0.00109318546569462
GO:0043296apical junction complex0.00109318546569462
GO:0016327apicolateral plasma membrane0.00109318546569462
GO:0005911intercellular junction0.00222815365861779
GO:0001892embryonic placenta development0.00546259906066675
GO:0030054cell junction0.00907390042342841
GO:0044459plasma membrane part0.00956535539574324
GO:0001890placenta development0.0127967491689525
GO:0016338calcium-independent cell-cell adhesion0.0166780129869154
GO:0001763morphogenesis of a branching structure0.0218233954500037
GO:0005886plasma membrane0.0262091988801033
GO:0019897extrinsic to plasma membrane0.0262091988801033
GO:0001701in utero embryonic development0.0262091988801033
GO:0016324apical plasma membrane0.0330721699696492
GO:0045177apical part of cell0.0380048061144456
GO:0009792embryonic development ending in birth or egg hatching0.0380048061144456
GO:0043009chordate embryonic development0.0380048061144456
GO:0019898extrinsic to membrane0.0404059085111664



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
endoderm-derived structure6.11e-25160
endoderm6.11e-25160
presumptive endoderm6.11e-25160
digestive system1.92e-19145
digestive tract1.92e-19145
primitive gut1.92e-19145
subdivision of digestive tract2.22e-18118
respiratory system1.11e-1274
anatomical space1.44e-1295
immaterial anatomical entity2.01e-12117
endo-epithelium5.67e-1282
foregut2.29e-1187
renal system2.70e-1148
trunk region element3.00e-11101
urinary system structure7.70e-1147
epithelial bud1.15e-0937
respiratory tract5.16e-0954
orifice5.87e-0936
organ2.59e-08503
thoracic cavity element2.61e-0834
thoracic cavity2.61e-0834
reproductive structure2.85e-0859
reproductive system2.85e-0859
subdivision of trunk3.35e-08112
nephron tubule epithelium6.93e-0810
thoracic segment organ7.17e-0835
epithelial fold9.77e-0847
male organism3.03e-0722
male reproductive system3.03e-0722
organism subdivision3.57e-07264
reproductive organ5.88e-0748
Disease
Ontology termp-valuen
carcinoma1.63e-17106
squamous cell carcinoma1.67e-1014
cell type cancer1.73e-10143
adenocarcinoma9.09e-0825


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
E2F1#186954.089491012399440.001749817597761990.0107556471127458
POLR2A#543062.147453176558070.01019570676818780.0379943416528497
SUZ12#23512216.70526030368760.005660234682079570.0255576848232472
TAF1#687263.343046285745290.0007162474284635620.00572641546209186
ZEB1#6935616.88843201754394.30431371220266e-082.827284401187e-06



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.