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Coexpression cluster:C938

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Full id: C938_leiomyoma_Smooth_Preadipocyte_hepatic_basal_Adipocyte_Ewing



Phase1 CAGE Peaks

Hg19::chr22:38864041..38864150,+p1@KDELR3
Hg19::chr2:242212239..242212257,-p1@HDLBP
Hg19::chr2:47142884..47142955,-p1@MCFD2
Hg19::chr3:57583064..57583079,-p1@ARF4
Hg19::chr3:57583085..57583121,-p2@ARF4
Hg19::chr3:57583130..57583152,-p3@ARF4
Hg19::chr4:38869366..38869387,+p3@FAM114A1
Hg19::chr4:38869393..38869404,+p2@FAM114A1
Hg19::chr4:38869410..38869435,+p1@FAM114A1


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


GO IDGO nameFDR corrected p-value
GO:0016192vesicle-mediated transport0.00428373742142871
GO:0015031protein transport0.00428373742142871
GO:0045184establishment of protein localization0.00428373742142871
GO:0008104protein localization0.00428373742142871
GO:0033036macromolecule localization0.00428373742142871
GO:0005737cytoplasm0.00733327368124839
GO:0006810transport0.00972679873071346
GO:0051234establishment of localization0.00972679873071346
GO:0046923ER retention sequence binding0.00972679873071346
GO:0006621protein retention in ER0.0104499899438909
GO:0051179localization0.0104499899438909
GO:0005048signal sequence binding0.0213109713755608
GO:0032507maintenance of cellular protein localization0.0213109713755608
GO:0051651maintenance of cellular localization0.0213109713755608
GO:0045185maintenance of protein localization0.0213109713755608
GO:0005794Golgi apparatus0.0213109713755608
GO:0051235maintenance of localization0.0298119136755056
GO:0005793ER-Golgi intermediate compartment0.0298119136755056
GO:0005783endoplasmic reticulum0.0301261191994913
GO:0044424intracellular part0.0342977698170602
GO:0008203cholesterol metabolic process0.0462566618772057



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>


Uber Anatomy
Ontology termp-valuen
unilaminar epithelium7.81e-24148
trunk mesenchyme5.73e-23122
organism subdivision7.31e-23264
somite8.00e-2371
presomitic mesoderm8.00e-2371
presumptive segmental plate8.00e-2371
dermomyotome8.00e-2371
trunk paraxial mesoderm8.00e-2371
mesenchyme1.00e-22160
entire embryonic mesenchyme1.00e-22160
dense mesenchyme tissue1.19e-2273
epithelial vesicle1.36e-2278
multilaminar epithelium1.94e-2283
paraxial mesoderm4.31e-2272
presumptive paraxial mesoderm4.31e-2272
trunk1.99e-20199
skeletal muscle tissue2.77e-2062
striated muscle tissue2.77e-2062
myotome2.77e-2062
epithelial tube3.17e-20117
vasculature1.28e-1978
vascular system1.28e-1978
muscle tissue1.73e-1964
musculature1.73e-1964
musculature of body1.73e-1964
splanchnic layer of lateral plate mesoderm5.82e-1983
artery2.15e-1742
arterial blood vessel2.15e-1742
arterial system2.15e-1742
vessel4.36e-1768
epithelial tube open at both ends5.69e-1759
blood vessel5.69e-1759
blood vasculature5.69e-1759
vascular cord5.69e-1759
multi-cellular organism2.45e-15656
systemic artery1.20e-1433
systemic arterial system1.20e-1433
cardiovascular system1.99e-13109
cell layer4.74e-13309
circulatory system5.87e-13112
anatomical system6.01e-13624
anatomical group6.53e-13625
multi-tissue structure9.62e-13342
surface structure1.00e-1299
epithelium2.15e-12306
integument3.61e-0946
integumental system3.61e-0946
anatomical cluster4.44e-09373
mesoderm1.12e-08315
mesoderm-derived structure1.12e-08315
presumptive mesoderm1.12e-08315
anatomical conduit1.86e-08240
skin of body5.42e-0841
aorta6.63e-0821
aortic system6.63e-0821
embryonic structure6.37e-07564
organ component layer8.41e-0766
developing anatomical structure8.41e-07581
Disease
Ontology termp-valuen
ovarian cancer2.36e-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
ATF3#46737.487724842002920.006050357420552810.0268411043515893
BATF#1053838.119267264101210.004821448895817150.0226242216484812
BRCA1#67236.728076881074590.008149333567200950.0321804389150371
CCNT2#90585.632179179522342.97597445628313e-060.000101075706094229
CHD2#110644.597343481829710.007379358397557620.0304971236469677
CTCFL#14069036.582158119658120.008659511962914930.032961249722825
E2F1#186984.36212374655942.18983367577486e-050.000481380844589036
E2F4#187445.630249029015310.003536571815964610.0179473286631452
E2F6#187673.902232235764630.0003067423599492730.00316341121069835
EGR1#195873.8796948515190.0003186557858542290.00326275408027744
ELK4#200547.215858514874680.001409539058987380.00916573375142164
ETS1#211377.566814050601823.61164439627206e-060.000118689908465153
GABPB1#255353.926491020101210.004337976092287310.0205868080657243
HEY1#2346294.040111043105713.4850025352467e-060.000116024921829337
HMGN3#932476.361092673717131.17234969197953e-050.000298122789093379
MAFF#23764318.77178549664840.0004336934263990230.00404921399603858
MAFK#797539.033577712609970.003567854712813750.0180841144553048
MEF2A#420536.247743636548020.01000005008462560.0374993799428462
NFYB#480135.586597751178820.01358500277111940.0479536318117056
NRF1#489945.426790865649290.004046698912068520.0193672984913172
POLR2A#543092.147453176558070.001029412892608020.00728936559028337
REST#597844.288901651612450.009457025945962830.0356692789010622
RFX5#599345.354627034308930.004249445027674740.0202217974778021
SIX5#14791235.6955717851530.01288794699034820.0463563953617915
SRF#672269.19811884144521.00386889165062e-050.000263094261418065
TAF1#687293.343046285745291.91655056102793e-050.000433627868377809
TFAP2C#702244.804101604382320.006299303434747120.0277885090357573
THAP1#55145310.45638153428380.002353923504026620.0133413695575534
ZBTB7A#5134154.084394059931050.003634990312833990.0183753510785126
ZEB1#693535.629477339181290.01330488236341950.047039560228611



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.