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Coexpression cluster:C2080: Difference between revisions

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|full_id=C2080_mucinous_Fibroblast_epithelioid_Preadipocyte_Olfactory_prostate_acantholytic
|full_id=C2080_mucinous_Fibroblast_epithelioid_Preadipocyte_Olfactory_prostate_acantholytic
|id=C2080
|id=C2080
|ontology_enrichment_celltype=CL:0000055!5.63e-20!180;CL:0000057!3.81e-16!75;CL:0000220!4.32e-16!246;CL:0002321!1.96e-15!248;CL:0000222!4.90e-15!119;CL:0000076!2.02e-13!62;CL:0000066!2.27e-13!254;CL:0000548!1.29e-10!679;CL:0000004!1.29e-10!679;CL:0000255!1.29e-10!679;CL:0002620!2.36e-10!23;CL:0000012!7.34e-10!682;CL:0000213!3.73e-08!57;CL:0000215!3.73e-08!57;CL:0000680!2.16e-07!57;CL:0000056!2.16e-07!57;CL:0000355!2.16e-07!57;CL:0000187!9.37e-07!54
|ontology_enrichment_celltype=CL:0000057!4.42e-16!76;CL:0002321!1.28e-15!250;CL:0000222!2.53e-15!121;CL:0000076!1.05e-13!63;CL:0000066!9.83e-13!253;CL:0000548!1.34e-10!679;CL:0000255!1.34e-10!679;CL:0002620!4.51e-10!23;CL:0000213!4.08e-08!58;CL:0000215!4.08e-08!58;CL:0000680!1.25e-07!58;CL:0000056!1.25e-07!58;CL:0000355!1.25e-07!58;CL:0000187!5.20e-07!55
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002100!2.09e-16!216;UBERON:0000468!3.09e-16!659;UBERON:0003102!9.07e-15!95;UBERON:0000475!2.31e-14!365;UBERON:0000467!9.50e-14!625;UBERON:0000480!2.03e-13!626;UBERON:0003104!8.58e-12!238;UBERON:0009142!8.58e-12!238;UBERON:0000914!1.06e-11!83;UBERON:0002329!1.06e-11!83;UBERON:0003077!1.06e-11!83;UBERON:0003059!1.06e-11!83;UBERON:0007282!1.06e-11!83;UBERON:0009618!1.06e-11!83;UBERON:0007285!1.06e-11!83;UBERON:0005256!1.92e-11!143;UBERON:0000926!6.75e-11!448;UBERON:0004120!6.75e-11!448;UBERON:0006603!6.75e-11!448;UBERON:0002049!3.59e-10!79;UBERON:0007798!3.59e-10!79;UBERON:0002097!9.26e-10!40;UBERON:0000486!2.28e-09!82;UBERON:0002199!2.71e-09!45;UBERON:0002416!2.71e-09!45;UBERON:0000490!5.53e-09!138;UBERON:0004290!6.13e-09!70;UBERON:0000481!8.84e-09!347;UBERON:0000055!6.72e-08!69;UBERON:0000062!1.30e-07!511;UBERON:0001981!1.39e-07!60;UBERON:0007500!1.39e-07!60;UBERON:0004537!1.39e-07!60;UBERON:0006965!1.39e-07!60;UBERON:0004872!1.63e-07!84;UBERON:0002050!2.47e-07!605;UBERON:0005423!2.47e-07!605;UBERON:0000923!3.93e-07!604;UBERON:0005291!3.93e-07!604;UBERON:0006598!3.93e-07!604;UBERON:0002532!3.93e-07!604;UBERON:0004923!3.94e-07!57;UBERON:0002385!8.88e-07!63;UBERON:0001015!8.88e-07!63;UBERON:0000383!8.88e-07!63;UBERON:0000922!8.94e-07!612
|ontology_enrichment_uberon=UBERON:0000475!3.25e-17!264;UBERON:0000468!2.08e-15!656;UBERON:0003102!2.76e-15!99;UBERON:0002100!7.86e-14!199;UBERON:0000467!9.08e-14!624;UBERON:0000480!1.91e-13!625;UBERON:0000490!3.39e-11!148;UBERON:0003104!2.92e-10!160;UBERON:0009142!2.92e-10!160;UBERON:0002049!4.33e-10!78;UBERON:0007798!4.33e-10!78;UBERON:0002097!5.68e-10!41;UBERON:0000486!9.96e-10!83;UBERON:0004923!1.74e-09!66;UBERON:0002199!1.89e-09!46;UBERON:0002416!1.89e-09!46;UBERON:0007524!3.52e-09!73;UBERON:0002329!3.52e-09!71;UBERON:0003059!3.52e-09!71;UBERON:0007282!3.52e-09!71;UBERON:0004290!3.52e-09!71;UBERON:0009618!3.52e-09!71;UBERON:0005256!6.00e-09!122;UBERON:0003077!7.58e-09!72;UBERON:0007285!7.58e-09!72;UBERON:0007503!7.72e-09!78;UBERON:0000055!8.24e-08!68;UBERON:0004872!1.79e-07!83;UBERON:0007500!1.99e-07!59;UBERON:0001981!1.99e-07!59;UBERON:0004537!1.99e-07!59;UBERON:0006965!1.99e-07!59;UBERON:0002385!5.30e-07!64;UBERON:0001015!5.30e-07!64;UBERON:0000383!5.30e-07!64;UBERON:0001134!6.80e-07!62;UBERON:0002036!6.80e-07!62;UBERON:0003082!6.80e-07!62
|tf_chipseq_enrich=BCL11A#53335;4:28.3694551036071:1.542446414682e-06:5.88140055140466e-05!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00815385886117955!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00433424572008082!ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.59233791851798e-05!GTF2B#2959;4:31.9438299343242:9.59435337635006e-07:4.07824449439408e-05!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.000716187200692898!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.00074141929183926!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386628372808676!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00484332037098994!MEF2A#4205;4:18.7432309096441:8.0978922767748e-06:0.000224154723428063!MEF2C#4208;4:41.3113544926241:3.42889182145094e-07:1.69720394758538e-05!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142072970899464!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129043803132742!SMARCC1#6599;4:43.6633593196315:2.74744977017458e-07:1.40519542873293e-05!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000436956539992418!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00248981268851225!STAT1#6772;4:20.7065874971992:5.43610708103893e-06:0.000164897353307181!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00122837743469364!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321121341304875!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243409638107046!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000325742982022192!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114319278276636!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000229603904697944
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}}
}}

Revision as of 12:02, 19 October 2012


Full id: C2080_mucinous_Fibroblast_epithelioid_Preadipocyte_Olfactory_prostate_acantholytic



Phase1 CAGE Peaks

Hg19::chr10:95241966..95241996,-p4@MYOF
Hg19::chr10:95242030..95242041,-p6@MYOF
Hg19::chr10:95242044..95242072,-p1@MYOF
Hg19::chr10:95242083..95242098,-p2@MYOF


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>

Cell Type
Ontology termp-valuen
fibroblast4.42e-1676
embryonic cell1.28e-15250
mesodermal cell2.53e-15121
squamous epithelial cell1.05e-1363
epithelial cell9.83e-13253
animal cell1.34e-10679
eukaryotic cell1.34e-10679
skin fibroblast4.51e-1023
lining cell4.08e-0858
barrier cell4.08e-0858
muscle precursor cell1.25e-0758
myoblast1.25e-0758
multi-potent skeletal muscle stem cell1.25e-0758
muscle cell5.20e-0755
Uber Anatomy
Ontology termp-valuen
organism subdivision3.25e-17264
multi-cellular organism2.08e-15656
surface structure2.76e-1599
trunk7.86e-14199
anatomical system9.08e-14624
anatomical group1.91e-13625
unilaminar epithelium3.39e-11148
mesenchyme2.92e-10160
entire embryonic mesenchyme2.92e-10160
vasculature4.33e-1078
vascular system4.33e-1078
skin of body5.68e-1041
multilaminar epithelium9.96e-1083
organ component layer1.74e-0966
integument1.89e-0946
integumental system1.89e-0946
dense mesenchyme tissue3.52e-0973
somite3.52e-0971
presomitic mesoderm3.52e-0971
presumptive segmental plate3.52e-0971
dermomyotome3.52e-0971
trunk paraxial mesoderm3.52e-0971
trunk mesenchyme6.00e-09122
paraxial mesoderm7.58e-0972
presumptive paraxial mesoderm7.58e-0972
epithelial vesicle7.72e-0978
vessel8.24e-0868
splanchnic layer of lateral plate mesoderm1.79e-0783
epithelial tube open at both ends1.99e-0759
blood vessel1.99e-0759
blood vasculature1.99e-0759
vascular cord1.99e-0759
muscle tissue5.30e-0764
musculature5.30e-0764
musculature of body5.30e-0764
skeletal muscle tissue6.80e-0762
striated muscle tissue6.80e-0762
myotome6.80e-0762


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
BCL11A#53335428.36945510360711.542446414682e-065.88140055140466e-05
CTCF#1066445.360256373075030.001211145381643620.00815385886117955
EP300#203346.77394172622320.0004748459821442640.00433424572008082
ESR1#2099430.76860329615451.11467714392546e-064.59233791851798e-05
GTF2B#2959431.94382993432429.59435337635006e-074.07824449439408e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.000716187200692898
JUN#3725412.51282919233634.07770316866756e-050.00074141929183926
JUND#372735.245997956403270.01043432751748420.0386628372808676
MAX#414946.452555509007120.0005767613195645490.00484332037098994
MEF2A#4205418.74323090964418.0978922767748e-060.000224154723428063
MEF2C#4208441.31135449262413.42889182145094e-071.69720394758538e-05
MXI1#460149.96157162875930.0001015224754950450.00142072970899464
RAD21#5885410.35503389545638.6948481184721e-050.00129043803132742
SMARCC1#6599443.66335931963152.74744977017458e-071.40519542873293e-05
SMC3#9126415.04493284493281.95092670935632e-050.000436956539992418
SPI1#668848.204323508522730.000220661881527680.00248981268851225
STAT1#6772420.70658749719925.43610708103893e-060.000164897353307181
STAT3#6774410.51946499715428.16377768286615e-050.00122837743469364
TAF1#687243.343046285745290.008005664898701650.0321121341304875
TBP#690843.706770687096390.005296377814784350.0243409638107046
TFAP2A#7020416.5186343730451.34240829060362e-050.000325742982022192
TFAP2C#7022410.80922860986027.32289634782688e-050.00114319278276636
TRIM28#10155418.59052504526258.36730015875654e-060.000229603904697944



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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