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Coexpression cluster:C1088

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Full id: C1088_liver_giant_anaplastic_glassy_bile_Hepatocyte_prostate



Phase1 CAGE Peaks

Hg19::chr6:64237703..64237708,+p@chr6:64237703..64237708
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Hg19::chr6:64237756..64237769,+p@chr6:64237756..64237769
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Hg19::chr6:64237780..64237794,+p@chr6:64237780..64237794
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Hg19::chr6:64237801..64237820,+p@chr6:64237801..64237820
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Hg19::chr6:64237829..64237843,+p@chr6:64237829..64237843
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Hg19::chr6:64237863..64237874,+p@chr6:64237863..64237874
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Hg19::chr6:64237875..64237910,+p@chr6:64237875..64237910
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Hg19::chr6:64237919..64237932,+p@chr6:64237919..64237932
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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
epithelial cell1.18e-15254
endodermal cell9.12e-1359
endo-epithelial cell7.18e-1043
respiratory epithelial cell5.20e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.24e-21169
endoderm1.24e-21169
presumptive endoderm1.24e-21169
digestive system1.05e-17155
digestive tract1.05e-17155
primitive gut1.05e-17155
respiratory system2.83e-1572
mixed endoderm/mesoderm-derived structure3.68e-15130
endo-epithelium3.91e-1582
subdivision of digestive tract1.06e-14129
endodermal part of digestive tract1.06e-14129
mesenchyme2.04e-13238
entire embryonic mesenchyme2.04e-13238
foregut3.06e-1398
respiratory tract1.14e-1153
trunk5.13e-11216
gland5.38e-1159
organism subdivision3.80e-10365
gut epithelium4.36e-1054
multi-tissue structure1.24e-09347
respiratory primordium1.32e-0938
endoderm of foregut1.32e-0938
segment of respiratory tract1.56e-0946
larynx8.96e-099
immaterial anatomical entity4.55e-08126
orifice4.65e-0835
exocrine gland5.52e-0831
exocrine system5.52e-0831
primordium1.19e-07168
epithelial bud1.81e-0737
subdivision of trunk3.85e-07113
epithelial sac4.60e-0725
epithelium of foregut-midgut junction7.96e-0725
anatomical boundary7.96e-0725
hepatobiliary system7.96e-0725
foregut-midgut junction7.96e-0725
septum transversum7.96e-0725
upper respiratory tract8.25e-0719
Disease
Ontology termp-valuen
carcinoma8.66e-18106
cell type cancer2.40e-13143


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
ATF3#467822.46317452600871.53751153688198e-111.87808382924464e-09
BHLHE40#8553844.87181354697746.04397679531981e-149.72614626388914e-12
BRCA1#672820.18423064322383.61942729088439e-114.1448395486039e-09
CEBPB#105187.971147625824826.12878626083745e-083.7987199305377e-06
ELF1#199784.258097958807549.24826870984006e-060.000246523720211074
EP300#203386.77394172622322.25366016107097e-071.19174690411185e-05
FOS#235388.99795530889442.32446530602145e-081.63808928539524e-06
FOSL2#2355816.93020060456171.47793326491323e-101.56545509385672e-08
FOXA1#3169811.08141974938554.39110036332964e-093.56057555004491e-07
FOXA2#3170824.63046375266527.35637804493982e-129.33527055450146e-10
GTF2F1#2962812.73966087675771.43868108630934e-091.2831290689416e-07
HDAC2#3066813.41562023662639.51254966654288e-108.87036763057207e-08
HEY1#2346284.040111043105711.4081650274634e-050.000339255703121685
HNF4A#3172823.13229036295371.21561011047446e-111.50959695990299e-09
JUN#3725812.51282919233631.66110954195842e-091.45662988625185e-07
JUND#372786.994663941871031.74369580801501e-079.57968682237137e-06
MAX#414986.452555509007123.32496617557502e-071.65992419890478e-05
NR3C1#2908814.9730233311733.9500670680339e-103.89557180848341e-08
POLR2A#543082.147453176558070.002210725788971910.0127251978987234
RAD21#5885810.35503389545637.55391711153941e-095.84821014982998e-07
RXRA#6256820.07461713913333.7806502647693e-114.31999270243152e-09
SMARCC1#6599843.66335931963157.52062965894322e-141.19187714863486e-11
SMC3#9126815.04493284493283.80148882898722e-103.77398946588019e-08
SP1#666785.69838137814098.98832477855329e-073.86627533586214e-05
SPI1#668866.153242631392047.3612205654473e-050.00114866056272934
STAT1#6772820.70658749719922.95008695392417e-113.42718722336915e-09
STAT3#6774810.51946499715426.65923543127245e-095.22527339749559e-07
TBP#690883.706770687096392.80450451364125e-050.000592434560882237
TCF7L2#6934810.77017656313735.51536816569572e-094.40381908147626e-07
TRIM28#10155818.59052504526256.99051420669847e-117.70129022398082e-09
USF1#739186.361499277207963.72538670743375e-071.83353281026236e-05



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.