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Coexpression cluster:C2080: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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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

Revision as of 14:45, 12 September 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
non-terminally differentiated cell5.63e-20180
fibroblast3.81e-1675
embryonic cell1.96e-15248
mesodermal cell4.90e-15119
squamous epithelial cell2.02e-1362
epithelial cell2.27e-13254
animal cell1.29e-10679
eukaryotic cell1.29e-10679
skin fibroblast2.36e-1023
lining cell3.73e-0857
barrier cell3.73e-0857
muscle precursor cell2.16e-0757
myoblast2.16e-0757
multi-potent skeletal muscle stem cell2.16e-0757
muscle cell9.37e-0754
Uber Anatomy
Ontology termp-valuen
trunk2.09e-16216
multi-cellular organism3.09e-16659
surface structure9.07e-1595
organism subdivision2.31e-14365
anatomical system9.50e-14625
anatomical group2.03e-13626
mesenchyme8.58e-12238
entire embryonic mesenchyme8.58e-12238
somite1.06e-1183
paraxial mesoderm1.06e-1183
presomitic mesoderm1.06e-1183
presumptive segmental plate1.06e-1183
trunk paraxial mesoderm1.06e-1183
presumptive paraxial mesoderm1.06e-1183
trunk mesenchyme1.92e-11143
mesoderm6.75e-11448
mesoderm-derived structure6.75e-11448
presumptive mesoderm6.75e-11448
vasculature3.59e-1079
vascular system3.59e-1079
skin of body9.26e-1040
multilaminar epithelium2.28e-0982
integument2.71e-0945
integumental system2.71e-0945
unilaminar epithelium5.53e-09138
dermomyotome6.13e-0970
multi-tissue structure8.84e-09347
vessel6.72e-0869
organ1.30e-07511
blood vessel1.39e-0760
epithelial tube open at both ends1.39e-0760
blood vasculature1.39e-0760
vascular cord1.39e-0760
splanchnic layer of lateral plate mesoderm1.63e-0784
embryonic structure2.47e-07605
developing anatomical structure2.47e-07605
germ layer3.93e-07604
embryonic tissue3.93e-07604
presumptive structure3.93e-07604
epiblast (generic)3.93e-07604
organ component layer3.94e-0757
muscle tissue8.88e-0763
musculature8.88e-0763
musculature of body8.88e-0763
embryo8.94e-07612


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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