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Coexpression cluster:C4123

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Full id: C4123_Neural_Melanocyte_Neurons_epithelioid_Wilms_Pericytes_leiomyoblastoma



Phase1 CAGE Peaks

Hg19::chr2:12857878..12857905,+p3@TRIB2
Hg19::chr2:12857930..12857961,+p5@TRIB2
Hg19::chr2:12857966..12857988,+p8@TRIB2


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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.38e-09180
mature alpha-beta T cell1.64e-0818
alpha-beta T cell1.64e-0818
immature T cell1.64e-0818
mature T cell1.64e-0818
immature alpha-beta T cell1.64e-0818
neurectodermal cell6.63e-0759
Uber Anatomy
Ontology termp-valuen
central nervous system1.33e-1182
regional part of nervous system1.76e-1194
nervous system1.76e-1194
adult organism2.05e-08115
regional part of brain6.00e-0859
neural tube2.38e-0757
neural rod2.38e-0757
future spinal cord2.38e-0757
neural keel2.38e-0757
brain2.44e-0769
future brain2.44e-0769


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#90536.336201576962630.003930750035764890.019042749929736
CTCF#1066435.360256373075030.0064925092527670.0280032697550893
E2F6#187635.017155731697390.00791769806886330.0323026863789216
RAD21#5885310.35503389545630.0009004912073565420.00665344189636433
SIN3A#2594235.408884726815140.006318961977991520.0277381502193786
THAP1#55145331.36914460285133.23800758564397e-050.000647967568953958
ZBTB7A#5134137.35190930787590.002516255860282270.0140517188424778



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.