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Coexpression cluster:C2423: Difference between revisions

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|full_id=C2423_small_signet_papillotubular_malignant_hepatocellular_maxillary_colon
|full_id=C2423_small_signet_papillotubular_malignant_hepatocellular_maxillary_colon
|id=C2423
|id=C2423
|ontology_enrichment_celltype=CL:0000066!4.37e-22!254;CL:0000223!8.34e-19!59;CL:0002076!3.92e-15!43;CL:0002251!1.67e-09!21;CL:0002368!2.61e-07!13
|ontology_enrichment_celltype=CL:0000223!1.25e-22!58;CL:0000066!2.75e-22!253;CL:0002076!1.56e-18!42;CL:0002251!8.66e-12!20;CL:0002368!2.87e-08!13
|ontology_enrichment_disease=DOID:305!3.02e-24!106;DOID:0050687!5.79e-16!143;DOID:1749!9.61e-09!14;DOID:162!1.58e-08!235;DOID:14566!1.17e-07!239;DOID:299!1.69e-07!25
|ontology_enrichment_disease=DOID:305!4.14e-24!106;DOID:0050687!1.31e-16!143;DOID:1749!1.67e-09!14;DOID:162!1.98e-08!235;DOID:14566!1.12e-07!239;DOID:299!4.30e-07!25;DOID:3119!9.70e-07!14
|ontology_enrichment_uberon=UBERON:0004119!4.26e-26!169;UBERON:0000925!4.26e-26!169;UBERON:0006595!4.26e-26!169;UBERON:0001007!1.02e-21!155;UBERON:0001555!1.02e-21!155;UBERON:0007026!1.02e-21!155;UBERON:0004921!5.01e-21!129;UBERON:0004185!5.01e-21!129;UBERON:0007023!7.39e-21!115;UBERON:0000077!7.40e-19!130;UBERON:0001041!1.05e-15!98;UBERON:0001004!3.64e-15!72;UBERON:0005911!8.89e-15!82;UBERON:0000064!1.97e-13!219;UBERON:0000481!3.36e-13!347;UBERON:0000065!1.11e-12!53;UBERON:0000062!5.12e-12!511;UBERON:0001048!3.65e-10!168;UBERON:0005177!3.70e-10!107;UBERON:0000466!6.51e-10!126;UBERON:0000063!7.28e-10!97;UBERON:0008947!1.04e-09!38;UBERON:0003258!1.04e-09!38;UBERON:0001049!1.46e-09!57;UBERON:0005068!1.46e-09!57;UBERON:0006241!1.46e-09!57;UBERON:0007135!1.46e-09!57;UBERON:0000072!1.91e-09!46;UBERON:0000153!1.96e-09!129;UBERON:0007811!1.96e-09!129;UBERON:0002530!3.39e-09!59;UBERON:0000033!1.36e-08!123;UBERON:0002365!3.24e-08!31;UBERON:0002330!3.24e-08!31;UBERON:0004111!3.69e-08!241;UBERON:0005153!5.29e-08!37;UBERON:0004121!5.74e-08!169;UBERON:0003929!6.80e-08!54;UBERON:0009569!8.38e-08!113;UBERON:0000924!1.78e-07!173;UBERON:0006601!1.78e-07!173;UBERON:0005178!1.88e-07!34;UBERON:0002224!1.88e-07!34;UBERON:0005157!2.38e-07!51;UBERON:0002616!2.54e-07!59;UBERON:0000475!2.92e-07!365;UBERON:0000477!3.65e-07!286;UBERON:0003075!3.91e-07!86;UBERON:0007284!3.91e-07!86;UBERON:0000464!4.24e-07!104;UBERON:0002048!5.68e-07!22;UBERON:0000117!5.68e-07!22;UBERON:0000171!5.68e-07!22;UBERON:0000170!5.68e-07!22;UBERON:0005597!5.68e-07!22;UBERON:0000118!5.68e-07!22;UBERON:0005181!5.82e-07!35
|ontology_enrichment_uberon=UBERON:0004119!4.45e-28!160;UBERON:0000925!4.45e-28!160;UBERON:0006595!4.45e-28!160;UBERON:0001007!7.24e-24!145;UBERON:0001555!7.24e-24!145;UBERON:0007026!7.24e-24!145;UBERON:0004921!1.36e-23!118;UBERON:0011216!7.94e-22!223;UBERON:0001041!3.66e-17!87;UBERON:0007023!6.31e-17!114;UBERON:0005911!2.85e-14!82;UBERON:0001004!8.25e-14!74;UBERON:0000481!8.68e-13!342;UBERON:0000062!1.15e-12!503;UBERON:0000477!1.19e-11!373;UBERON:0000065!7.69e-11!54;UBERON:0005177!1.95e-10!101;UBERON:0000064!4.73e-10!218;UBERON:0000466!7.57e-10!117;UBERON:0002365!2.10e-09!31;UBERON:0002330!2.10e-09!31;UBERON:0001048!2.55e-09!160;UBERON:0002530!4.65e-09!59;UBERON:0008947!9.95e-09!38;UBERON:0003258!9.95e-09!38;UBERON:0003929!1.57e-08!54;UBERON:0000063!2.04e-08!98;UBERON:0005409!7.93e-08!25;UBERON:0000072!1.46e-07!47;UBERON:0009569!2.93e-07!112;UBERON:0010371!4.57e-07!104;UBERON:0005153!6.42e-07!37;UBERON:0004111!8.45e-07!240
|tf_chipseq_enrich=BATF#10538;4:24.3578017923036:2.83869198020713e-06:9.7812653157655e-05!BCL11A#53335;4:28.3694551036071:1.542446414682e-06:5.89000223411238e-05!BCLAF1#9774;4:21.6526476101218:4.54636978835329e-06:0.000141609995325329!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512009501484403!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268011663546547!CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129025792841927!CTBP2#1488;4:62.7170003393281:6.45042639894877e-08:3.95349813779231e-06!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817071329458551!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199533089041517!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.01014069536803!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160837411931457!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434145491807448!FOSL2#2355;4:16.9302006045617:1.2165416097647e-05:0.000303522191070749!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00106995999347875!FOXA2#3170;4:24.6304637526652:2.71504128667089e-06:9.42047165909039e-05!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000721522045553435!GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.76976199839047e-05!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.00071787356794684!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000626410812439329!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185941370849511!HNF4A#3172;4:23.1322903629537:3.48990320893214e-06:0.000115525198490543!HSF1#3297;4:164.290666666667:1.36534966436082e-09:1.22821493192231e-07!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00307361278297232!IRF4#3662;4:21.9145126867441:4.33289161192893e-06:0.000136302068391038!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391549430255405!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485307568917192!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00887305371502808!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00767724559857358!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000442942598973795!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00443711999904702!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188352491629924!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129337878171928!REST#5978;4:9.65002871612802:0.000115282561421917:0.00156934247032633!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000826277463106179!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00795895072770701!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000241312082916041!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000437801535450075!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00683804387804609!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322036604535494!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.000968662660959406!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244054005117257!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.0012003047378266!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115382878624485!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114541855873999!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000230148133073578!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00507806057275302!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106795114794575!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000304066732326052!ZNF143#7702;4:13.5008765522279:3.00867915035614e-05:0.00062087224221309!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248720015530756
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}}
}}

Revision as of 14:00, 19 October 2012


Full id: C2423_small_signet_papillotubular_malignant_hepatocellular_maxillary_colon



Phase1 CAGE Peaks

Hg19::chr17:56494853..56494874,-p3@RNF43
Hg19::chr17:56494882..56494902,-p1@RNF43
Hg19::chr17:56494908..56494949,-p2@RNF43
Hg19::chr17:56494950..56494961,-p6@RNF43


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>

Cell Type
Ontology termp-valuen
endodermal cell1.25e-2258
epithelial cell2.75e-22253
endo-epithelial cell1.56e-1842
epithelial cell of alimentary canal8.66e-1220
respiratory epithelial cell2.87e-0813
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.45e-28160
endoderm4.45e-28160
presumptive endoderm4.45e-28160
digestive system7.24e-24145
digestive tract7.24e-24145
primitive gut7.24e-24145
subdivision of digestive tract1.36e-23118
organ system subdivision7.94e-22223
foregut3.66e-1787
adult organism6.31e-17114
endo-epithelium2.85e-1482
respiratory system8.25e-1474
multi-tissue structure8.68e-13342
organ1.15e-12503
anatomical cluster1.19e-11373
respiratory tract7.69e-1154
trunk region element1.95e-10101
organ part4.73e-10218
immaterial anatomical entity7.57e-10117
exocrine gland2.10e-0931
exocrine system2.10e-0931
primordium2.55e-09160
gland4.65e-0959
respiratory primordium9.95e-0938
endoderm of foregut9.95e-0938
gut epithelium1.57e-0854
organ segment2.04e-0898
gastrointestinal system7.93e-0825
segment of respiratory tract1.46e-0747
subdivision of trunk2.93e-07112
ecto-epithelium4.57e-07104
epithelial bud6.42e-0737
anatomical conduit8.45e-07240
Disease
Ontology termp-valuen
carcinoma4.14e-24106
cell type cancer1.31e-16143
squamous cell carcinoma1.67e-0914
cancer1.98e-08235
disease of cellular proliferation1.12e-07239
adenocarcinoma4.30e-0725
gastrointestinal system cancer9.70e-0714


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
BATF#10538424.35780179230362.83869198020713e-069.7812653157655e-05
BCL11A#53335428.36945510360711.542446414682e-065.89000223411238e-05
BCLAF1#9774421.65264761012184.54636978835329e-060.000141609995325329
CCNT2#90546.336201576962630.0006203100587215640.00512009501484403
CEBPB#105147.971147625824820.0002476385788090830.00268011663546547
CHD2#1106410.34402283411698.73193255208051e-050.00129025792841927
CTBP2#1488462.71700033932816.45042639894877e-083.95349813779231e-06
CTCF#1066445.360256373075030.001211145381643620.00817071329458551
EBF1#187948.9064668465690.00015887907472010.00199533089041517
EGR1#195844.988179094810140.001615011500076050.01014069536803
ELF1#199744.258097958807540.003041525565781240.0160837411931457
EP300#203346.77394172622320.0004748459821442640.00434145491807448
FOSL2#2355416.93020060456171.2165416097647e-050.000303522191070749
FOXA1#3169411.08141974938556.62943068949433e-050.00106995999347875
FOXA2#3170424.63046375266522.71504128667089e-069.42047165909039e-05
GATA2#2624412.7449317335543.78864877853583e-050.000721522045553435
GATA3#2625427.2365163572061.81561517799785e-066.76976199839047e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.00071787356794684
HDAC2#3066413.41562023662633.0859005065161e-050.000626410812439329
HEY1#2346244.040111043105710.00375304636917980.0185941370849511
HNF4A#3172423.13229036295373.48990320893214e-060.000115525198490543
HSF1#32974164.2906666666671.36534966436082e-091.22821493192231e-07
IRF1#365947.63716375356390.0002938853996185490.00307361278297232
IRF4#3662421.91451268674414.33289161192893e-060.000136302068391038
JUND#372746.994663941871030.000417684217818580.00391549430255405
MAX#414946.452555509007120.0005767613195645490.00485307568917192
MYC#460945.22228187160940.001344309395272740.00887305371502808
NFKB1#479045.488063424193840.001102199566301980.00767724559857358
NR3C1#2908414.9730233311731.98868032687801e-050.000442942598973795
PAX5#507946.669565531177830.0005052774169483260.00443711999904702
POU2F2#545249.106124057742520.000145395665174930.00188352491629924
RAD21#5885410.35503389545638.6948481184721e-050.00129337878171928
REST#597849.650028716128020.0001152825614219170.00156934247032633
RFX5#5993412.04791082719514.74457429336527e-050.000826277463106179
SIN3A#2594245.408884726815140.001168172384885160.00795895072770701
SMARCB1#6598418.25271578115749.00423392720929e-060.000241312082916041
SMC3#9126415.04493284493281.95092670935632e-050.000437801535450075
SP1#666745.69838137814090.0009482606065333980.00683804387804609
TAF1#687243.343046285745290.008005664898701650.0322036604535494
TAF7#6879411.43306940492395.85061525419808e-050.000968662660959406
TBP#690843.706770687096390.005296377814784350.0244054005117257
TCF12#6938410.63446490218647.8163066689251e-050.0012003047378266
TCF7L2#6934410.77017656313737.42969445082454e-050.00115382878624485
TFAP2C#7022410.80922860986027.32289634782688e-050.00114541855873999
TRIM28#10155418.59052504526258.36730015875654e-060.000230148133073578
USF1#739146.361499277207960.0006105011399140830.00507806057275302
YY1#752844.911170749853860.00171871838055440.0106795114794575
ZEB1#6935416.88843201754391.22862303393937e-050.000304066732326052
ZNF143#7702413.50087655222793.00867915035614e-050.00062087224221309
ZNF263#1012748.221841637010680.0002187871180958320.00248720015530756



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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