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Coexpression cluster:C1596

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Full id: C1596_heart_optic_left_corpus_substantia_spinal_medulla



Phase1 CAGE Peaks

Hg19::chr10:88426533..88426556,+p2@LDB3
Hg19::chr11:111781454..111781513,-p4@CRYAB
Hg19::chr20:44036838..44036847,+p22@DBNDD2
Hg19::chrX:10124977..10125036,+p2@CLCN4
Hg19::chrX:10125040..10125059,+p3@CLCN4


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:0032387negative regulation of intracellular transport0.0240187203952639



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism2.47e-51115
neural tube2.73e-2657
neural rod2.73e-2657
future spinal cord2.73e-2657
neural keel2.73e-2657
central nervous system5.87e-2682
regional part of nervous system1.23e-2594
nervous system1.23e-2594
neural plate6.63e-2486
presumptive neural plate6.63e-2486
brain8.55e-2469
future brain8.55e-2469
regional part of brain3.17e-2259
neurectoderm8.33e-2190
anterior neural tube1.62e-2042
regional part of forebrain5.33e-2041
forebrain5.33e-2041
future forebrain5.33e-2041
head4.86e-18123
anterior region of body1.30e-17129
craniocervical region1.30e-17129
ectoderm-derived structure1.34e-17169
pre-chordal neural plate1.30e-1661
telencephalon3.51e-1634
gray matter3.71e-1634
brain grey matter3.71e-1634
ectoderm7.32e-16173
presumptive ectoderm7.32e-16173
regional part of telencephalon1.42e-1533
cerebral hemisphere7.51e-1532
anatomical conduit2.85e-14241
tube1.96e-13194
organism subdivision4.11e-13365
anatomical cluster6.76e-13286
cerebral cortex7.93e-1125
pallium7.93e-1125
regional part of cerebral cortex1.36e-1022
multi-cellular organism2.21e-10659
epithelium4.52e-10309
cell layer5.22e-10312
neocortex1.70e-0920
anatomical group9.57e-09626
anatomical system1.41e-08625
multi-tissue structure2.46e-08347
organ9.69e-08511
nucleus of brain4.87e-079
neural nucleus4.87e-079
posterior neural tube5.50e-0715
chordal neural plate5.50e-0715
basal ganglion7.58e-079
nuclear complex of neuraxis7.58e-079
aggregate regional part of brain7.58e-079
collection of basal ganglia7.58e-079
cerebral subcortex7.58e-079


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
SETDB1#9869216.12801047120420.00585057846659340.0262661120436981



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.