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Coexpression cluster:C4467: Difference between revisions

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|full_id=C4467_Smooth_Fibroblast_Hepatocyte_pancreas_Mesenchymal_somatostatinoma_Adipocyte
|full_id=C4467_Smooth_Fibroblast_Hepatocyte_pancreas_Mesenchymal_somatostatinoma_Adipocyte
|id=C4467
|id=C4467
|ontology_enrichment_celltype=CL:0000055!9.13e-15!180;CL:0000183!2.81e-12!59;CL:0000192!7.73e-12!42;CL:0000514!7.73e-12!42;CL:0000680!2.46e-11!57;CL:0000056!2.46e-11!57;CL:0000355!2.46e-11!57;CL:0000222!4.56e-11!119;CL:0000187!1.26e-10!54;CL:0000359!9.84e-10!32;CL:0000057!6.42e-09!75;CL:0000220!9.80e-08!246;CL:0002321!3.99e-07!248;CL:0000393!7.81e-07!60;CL:0000211!7.81e-07!60
|ontology_enrichment_celltype=CL:0000183!2.80e-12!59;CL:0000192!1.08e-11!43;CL:0000514!1.08e-11!43;CL:0000680!2.09e-11!58;CL:0000056!2.09e-11!58;CL:0000355!2.09e-11!58;CL:0000222!4.17e-11!121;CL:0000187!1.07e-10!55;CL:0000359!3.29e-10!32;CL:0000057!7.01e-09!76;CL:0002321!5.60e-07!250;CL:0000393!5.66e-07!61;CL:0000211!5.66e-07!61
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005256!2.46e-15!143;UBERON:0002100!4.71e-15!216;UBERON:0000486!2.13e-12!82;UBERON:0004290!3.18e-12!70;UBERON:0000914!5.82e-12!83;UBERON:0002329!5.82e-12!83;UBERON:0003077!5.82e-12!83;UBERON:0003059!5.82e-12!83;UBERON:0007282!5.82e-12!83;UBERON:0009618!5.82e-12!83;UBERON:0007285!5.82e-12!83;UBERON:0001134!1.26e-11!61;UBERON:0002036!1.26e-11!61;UBERON:0003082!1.26e-11!61;UBERON:0003914!2.44e-11!118;UBERON:0002385!3.88e-11!63;UBERON:0001015!3.88e-11!63;UBERON:0000383!3.88e-11!63;UBERON:0003104!8.18e-11!238;UBERON:0009142!8.18e-11!238;UBERON:0000475!1.39e-10!365;UBERON:0009569!9.58e-10!113;UBERON:0001637!4.84e-09!42;UBERON:0003509!4.84e-09!42;UBERON:0004572!4.84e-09!42;UBERON:0000490!5.36e-09!138;UBERON:0000481!1.28e-08!347;UBERON:0000926!1.56e-08!448;UBERON:0004120!1.56e-08!448;UBERON:0006603!1.56e-08!448;UBERON:0004872!1.74e-08!84;UBERON:0000468!1.81e-08!659;UBERON:0002049!1.92e-08!79;UBERON:0007798!1.92e-08!79;UBERON:0004573!6.03e-08!33;UBERON:0004571!6.03e-08!33;UBERON:0000055!1.62e-07!69;UBERON:0000480!1.62e-07!626;UBERON:0002417!2.19e-07!61;UBERON:0000916!2.19e-07!61;UBERON:0001981!2.37e-07!60;UBERON:0007500!2.37e-07!60;UBERON:0004537!2.37e-07!60;UBERON:0006965!2.37e-07!60;UBERON:0000467!2.43e-07!625;UBERON:0000483!5.83e-07!309;UBERON:0000119!7.12e-07!312
|ontology_enrichment_uberon=UBERON:0003104!2.11e-16!160;UBERON:0009142!2.11e-16!160;UBERON:0005256!2.15e-15!122;UBERON:0007503!3.60e-14!78;UBERON:0002100!5.76e-14!199;UBERON:0000475!5.36e-13!264;UBERON:0007524!1.53e-12!73;UBERON:0000486!1.78e-12!83;UBERON:0002329!2.46e-12!71;UBERON:0003059!2.46e-12!71;UBERON:0007282!2.46e-12!71;UBERON:0004290!2.46e-12!71;UBERON:0009618!2.46e-12!71;UBERON:0003914!2.93e-12!117;UBERON:0003077!4.50e-12!72;UBERON:0007285!4.50e-12!72;UBERON:0001134!5.18e-12!62;UBERON:0002036!5.18e-12!62;UBERON:0003082!5.18e-12!62;UBERON:0002385!1.73e-11!64;UBERON:0001015!1.73e-11!64;UBERON:0000383!1.73e-11!64;UBERON:0000490!2.98e-10!148;UBERON:0001637!2.02e-09!42;UBERON:0003509!2.02e-09!42;UBERON:0004572!2.02e-09!42;UBERON:0000468!4.62e-09!656;UBERON:0009569!9.58e-09!112;UBERON:0004872!1.57e-08!83;UBERON:0002049!1.58e-08!78;UBERON:0007798!1.58e-08!78;UBERON:0000481!2.24e-08!342;UBERON:0000480!4.15e-08!625;UBERON:0000467!5.54e-08!624;UBERON:0004573!8.53e-08!33;UBERON:0004571!8.53e-08!33;UBERON:0007500!9.04e-08!59;UBERON:0001981!9.04e-08!59;UBERON:0004537!9.04e-08!59;UBERON:0006965!9.04e-08!59;UBERON:0000055!1.13e-07!68;UBERON:0002417!1.18e-07!60;UBERON:0000916!1.18e-07!60;UBERON:0000483!7.83e-07!306;UBERON:0000119!9.68e-07!309
|tf_chipseq_enrich=BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000285570923664139!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190825827632245!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00438475025568431!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323836486631687!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322022107459217!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464357332546613!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764384291112616!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154663255045109!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00389073940018112!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.010904270060133!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128590568720847!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270528126849892!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00472874685399941!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173505112493367!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00884914823128545!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667232360447746!REST#5978;3:9.65002871612802:0.00111263624711459:0.00770216855653216!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00240218156085892!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203720191357938!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247569619074491!SREBF1#6720;3:47.0058494404883:9.62099323994382e-06:0.000255286309193723!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00544850215231161!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631275361358669!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00616404315356511!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000648464571883165!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190954814947836!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330800778373462!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140735417871804!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00390318542480417
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}}
}}

Revision as of 15:58, 19 October 2012


Full id: C4467_Smooth_Fibroblast_Hepatocyte_pancreas_Mesenchymal_somatostatinoma_Adipocyte



Phase1 CAGE Peaks

Hg19::chr5:138533973..138534006,-p1@SIL1
Hg19::chr5:138534029..138534045,-p3@SIL1
Hg19::chr5:138534047..138534064,-p2@SIL1


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
mesenchyme2.11e-16160
entire embryonic mesenchyme2.11e-16160
trunk mesenchyme2.15e-15122
epithelial vesicle3.60e-1478
trunk5.76e-14199
organism subdivision5.36e-13264
dense mesenchyme tissue1.53e-1273
multilaminar epithelium1.78e-1283
somite2.46e-1271
presomitic mesoderm2.46e-1271
presumptive segmental plate2.46e-1271
dermomyotome2.46e-1271
trunk paraxial mesoderm2.46e-1271
epithelial tube2.93e-12117
paraxial mesoderm4.50e-1272
presumptive paraxial mesoderm4.50e-1272
skeletal muscle tissue5.18e-1262
striated muscle tissue5.18e-1262
myotome5.18e-1262
muscle tissue1.73e-1164
musculature1.73e-1164
musculature of body1.73e-1164
unilaminar epithelium2.98e-10148
artery2.02e-0942
arterial blood vessel2.02e-0942
arterial system2.02e-0942
multi-cellular organism4.62e-09656
subdivision of trunk9.58e-09112
splanchnic layer of lateral plate mesoderm1.57e-0883
vasculature1.58e-0878
vascular system1.58e-0878
multi-tissue structure2.24e-08342
anatomical group4.15e-08625
anatomical system5.54e-08624
systemic artery8.53e-0833
systemic arterial system8.53e-0833
epithelial tube open at both ends9.04e-0859
blood vessel9.04e-0859
blood vasculature9.04e-0859
vascular cord9.04e-0859
vessel1.13e-0768
abdominal segment of trunk1.18e-0760
abdomen1.18e-0760
epithelium7.83e-07306
cell layer9.68e-07309


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285570923664139
CCNT2#90536.336201576962630.003930750035764890.0190825827632245
E2F4#1874312.66806031528440.0004917987006298980.00438475025568431
E2F6#187635.017155731697390.00791769806886330.0323836486631687
EGR1#195834.988179094810140.008056488137383440.0322022107459217
ELF1#199734.258097958807540.01295179875054610.0464357332546613
ETS1#211339.728760922202340.001085840092584840.00764384291112616
GABPB1#255337.067683836182170.002832212825417420.0154663255045109
GATA1#2623313.56030814380040.0004009615963782630.00389073940018112
HMGN3#932438.178547723350590.001827766942164210.010904270060133
IRF1#365937.63716375356390.002244692747297240.0128590568720847
NFKB1#479035.488063424193840.006049381815655430.0270528126849892
NRF1#4899312.21027944771090.0005492172401020010.00472874685399941
PAX5#507936.669565531177830.003370290999677260.0173505112493367
POU2F2#545239.106124057742520.001324165192682130.00884914823128545
RAD21#5885310.35503389545630.0009004912073565420.00667232360447746
REST#597839.650028716128020.001112636247114590.00770216855653216
SIX5#147912317.0867153554590.0002004060546325010.00240218156085892
SMARCB1#6598318.25271578115740.000164397760679890.00203720191357938
SP1#666735.69838137814090.005403962701712170.0247569619074491
SREBF1#6720347.00584944048839.62099323994382e-060.000255286309193723
TAF7#6879311.43306940492390.0006690181981945830.00544850215231161
TCF12#6938310.63446490218640.0008313523990202070.00631275361358669
TCF7L2#6934310.77017656313730.0008003181298398380.00616404315356511
THAP1#55145331.36914460285133.23800758564397e-050.000648464571883165
USF1#739136.361499277207960.00388404057290560.0190954814947836
YY1#752834.911170749853860.008441455341808260.0330800778373462
ZBTB7A#5134137.35190930787590.002516255860282270.0140735417871804
ZNF143#7702313.50087655222790.0004062804962997170.00390318542480417



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.