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Coexpression cluster:C3678

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Full id: C3678_Mast_Mesenchymal_Renal_breast_Synoviocyte_myeloma_CD14



Phase1 CAGE Peaks

Hg19::chr17:73874625..73874640,-p3@TRIM47
Hg19::chr17:73874641..73874653,-p5@TRIM47
Hg19::chr17:73874654..73874675,-p1@TRIM47


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>


Uber Anatomy
Ontology termp-valuen
anatomical cluster4.48e-30373
anatomical conduit2.98e-25240
anatomical group5.56e-20625
anatomical system6.31e-20624
epithelium7.79e-20306
tube4.69e-19192
cell layer5.73e-19309
multi-tissue structure2.00e-17342
multi-cellular organism3.09e-17656
embryo9.14e-16592
developing anatomical structure2.24e-15581
adult organism9.70e-15114
embryonic structure9.45e-14564
germ layer1.98e-13560
germ layer / neural crest1.98e-13560
embryonic tissue1.98e-13560
presumptive structure1.98e-13560
germ layer / neural crest derived structure1.98e-13560
epiblast (generic)1.98e-13560
organ system subdivision3.10e-13223
organ part1.37e-12218
structure with developmental contribution from neural crest3.93e-12132
organ2.24e-11503
blood vessel endothelium2.54e-1018
endothelium2.54e-1018
cardiovascular system endothelium2.54e-1018
central nervous system2.93e-1081
epithelial tube5.03e-10117
neural tube8.07e-1056
neural rod8.07e-1056
future spinal cord8.07e-1056
neural keel8.07e-1056
compound organ1.95e-0968
neural plate2.29e-0982
presumptive neural plate2.29e-0982
ecto-epithelium2.41e-09104
squamous epithelium6.98e-0925
ectoderm-derived structure1.41e-08171
ectoderm1.41e-08171
presumptive ectoderm1.41e-08171
simple squamous epithelium1.58e-0822
regional part of nervous system1.78e-0853
regional part of brain1.78e-0853
nervous system2.64e-0889
brain5.70e-0868
future brain5.70e-0868
neurectoderm9.18e-0886
regional part of forebrain1.92e-0741
forebrain1.92e-0741
anterior neural tube1.92e-0741
future forebrain1.92e-0741
brain grey matter2.41e-0734
gray matter2.41e-0734
endoderm-derived structure3.49e-07160
endoderm3.49e-07160
presumptive endoderm3.49e-07160
telencephalon3.98e-0734
vessel8.87e-0768


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
CHD2#1106310.34402283411690.0009033701102746880.00660046669560502
CTCF#1066435.360256373075030.0064925092527670.0279213989643703
E2F1#186934.907389214879320.008460985347239390.0324993324266397
E2F6#187635.017155731697390.00791769806886330.032180746754904
EGR1#195834.988179094810140.008056488137383440.0320342482517395
MAFF#23764356.31535648994525.59409009993116e-060.000169002365040992
MXI1#460139.96157162875930.001011470541259020.00719744987794175
MYC#460935.22228187160940.007020843755740150.0294253341227877
ZBTB7A#5134137.35190930787590.002516255860282270.0140037965358638



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.