Personal tools

Coexpression cluster:C2841

From FANTOM5_SSTAR

Revision as of 13:11, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2841_sacrococcigeal_CD14_Smooth_colon_Prostate_anaplastic_tridermal



Phase1 CAGE Peaks

Hg19::chr6:123110302..123110313,+p4@SMPDL3A
Hg19::chr6:123110370..123110382,+p2@SMPDL3A
Hg19::chr6:123110389..123110441,+p1@SMPDL3A
Hg19::chr6:123110465..123110480,+p3@SMPDL3A


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
multi-cellular organism4.07e-26659
organ5.36e-23511
anatomical system1.61e-20625
anatomical group3.42e-20626
embryonic structure2.89e-19605
developing anatomical structure2.89e-19605
germ layer6.22e-19604
embryonic tissue6.22e-19604
presumptive structure6.22e-19604
epiblast (generic)6.22e-19604
embryo2.74e-18612
bone marrow2.63e-1380
bone element3.62e-1286
immune system3.85e-12115
skeletal element4.01e-11101
skeletal system4.01e-11101
musculoskeletal system6.84e-11167
adult organism2.59e-10115
hematopoietic system4.16e-10102
blood island4.16e-10102
mesoderm1.20e-09448
mesoderm-derived structure1.20e-09448
presumptive mesoderm1.20e-09448
hemolymphoid system5.35e-09112


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
E2F6#187645.017155731697390.00157802193473060.00998951587109522
HEY1#2346244.040111043105710.00375304636917980.0186534245348484
MAX#414946.452555509007120.0005767613195645490.00486287038459691
MYC#460945.22228187160940.001344309395272740.00889554133769812
RAD21#588537.766275421592250.0033411193858720.0172769801228443
TFAP2A#7020416.5186343730451.34240829060362e-050.000327187349970482
TFAP2C#7022410.80922860986027.32289634782688e-050.00114799755579509
TRIM28#10155418.59052504526258.36730015875654e-060.000230755865138731
USF1#739146.361499277207960.0006105011399140830.00508900379531383
USF2#7392412.99219738506963.50833029870167e-050.000682575462120163
YY1#752844.911170749853860.00171871838055440.0107030725029349



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.