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Coexpression cluster:C3883

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Full id: C3883_Reticulocytes_teratocarcinoma_Renal_transitionalcell_mesothelioma_Tracheal_Alveolar



Phase1 CAGE Peaks

Hg19::chr1:156721389..156721400,-p4@HDGF
Hg19::chr1:156721427..156721445,-p2@HDGF
Hg19::chr1:156721446..156721494,-p1@HDGF


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 cell3.13e-33254
embryonic cell7.03e-24248
animal cell2.56e-22679
eukaryotic cell2.56e-22679
squamous epithelial cell1.84e-1362
native cell6.08e-13722
mesodermal cell3.43e-11119
non-terminally differentiated cell1.98e-08180
lining cell2.08e-0857
barrier cell2.08e-0857
Uber Anatomy
Ontology termp-valuen
mesenchyme1.75e-13238
entire embryonic mesenchyme1.75e-13238
trunk2.01e-09216
endoderm-derived structure7.23e-09169
endoderm7.23e-09169
presumptive endoderm7.23e-09169
trunk mesenchyme2.87e-08143
epithelial tube4.75e-08118
unilaminar epithelium1.55e-07138
segment of respiratory tract1.92e-0746
respiratory primordium1.92e-0738
endoderm of foregut1.92e-0738
mixed endoderm/mesoderm-derived structure2.65e-07130
digestive system3.28e-07155
digestive tract3.28e-07155
primitive gut3.28e-07155
trunk region element5.22e-07107
Disease
Ontology termp-valuen
cancer1.85e-29235
disease of cellular proliferation1.07e-28239
cell type cancer7.80e-18143
carcinoma3.22e-16106
organ system cancer5.26e-12137
hematologic cancer5.05e-0851
immune system cancer5.05e-0851
leukemia2.99e-0739


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
CCNT2#90536.336201576962630.003930750035764890.0190101228518291
CHD2#1106310.34402283411690.0009033701102746880.00660555002079242
CTCF#1066435.360256373075030.0064925092527670.0279536288019843
E2F1#186934.907389214879320.008460985347239390.0325472135793862
E2F4#1874312.66806031528440.0004917987006298980.00437354942907748
E2F6#187635.017155731697390.00791769806886330.0322359452913618
EBF1#187938.9064668465690.00141523283560980.00915601202491807
EGR1#195834.988179094810140.008056488137383440.032076991520727
ELF1#199734.258097958807540.01295179875054610.0462468087698138
EP300#203336.77394172622320.003216880500103790.0167498146649885
ETS1#211339.728760922202340.001085840092584840.0076258525606528
FOXA1#3169311.08141974938550.000734755275698670.00581562002566831
GABPB1#255337.067683836182170.002832212825417420.0154179554482028
HDAC2#3066313.41562023662630.0004140761399857210.0039139920340274
HMGN3#932438.178547723350590.001827766942164210.0108750727324496
IRF1#365937.63716375356390.002244692747297240.0128140730163967
JUND#372736.994663941871030.002921845042734990.0156827307235173
MAX#414936.452555509007120.003721913834265510.0186594162316079
MXI1#460139.96157162875930.001011470541259020.00720432188900982
MYC#460935.22228187160940.007020843755740150.0294619857363286
NANOG#79923329.24477848101273.99627955670032e-050.00073778935941705
NFKB1#479035.488063424193840.006049381815655430.0269696656469409
NFYA#4800318.42558069983050.0001598135507814160.00199745900311876
NR2C2#7182332.61461090524092.88098172333076e-050.000605162611027638
PAX5#507936.669565531177830.003370290999677260.0172984972338949
SIN3A#2594235.408884726815140.006318961977991520.0276892703708759
SIX5#147912317.0867153554590.0002004060546325010.00239832794084608
SP1#666735.69838137814090.005403962701712170.0246617636270097
SRF#6722313.79717826216780.0003806615025800190.00375232719848557
TCF7L2#6934310.77017656313730.0008003181298398380.00614049553058646
USF1#739136.361499277207960.00388404057290560.0190345508607615
USF2#7392312.99219738506960.0004558979393427810.00421731841337651
YY1#752834.911170749853860.008441455341808260.0329551866941953
ZBTB7A#5134137.35190930787590.002516255860282270.014026219352691
ZNF143#7702313.50087655222790.0004062804962997170.00389208665869071
ZNF263#1012738.221841637010680.001799043925565870.0109461315783381



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.