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Coexpression cluster:C1792

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Full id: C1792_medial_Neutrophils_Whole_amygdala_occipital_spinal_brain



Phase1 CAGE Peaks

Hg19::chr17:73843026..73843066,-p4@WBP2
Hg19::chr17:73843605..73843662,-p2@WBP2
Hg19::chr17:73843947..73843961,-p3@WBP2
Hg19::chr17:73844722..73844751,-p@chr17:73844722..73844751
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Hg19::chr17:73845785..73845824,-p@chr17:73845785..73845824
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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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism3.93e-30114
neural tube3.40e-1956
neural rod3.40e-1956
future spinal cord3.40e-1956
neural keel3.40e-1956
regional part of nervous system1.17e-1753
regional part of brain1.17e-1753
neurectoderm5.29e-1586
neural plate6.74e-1582
presumptive neural plate6.74e-1582
regional part of forebrain7.91e-1541
forebrain7.91e-1541
anterior neural tube7.91e-1541
future forebrain7.91e-1541
central nervous system5.08e-1481
brain grey matter1.80e-1334
gray matter1.80e-1334
telencephalon5.19e-1334
regional part of telencephalon1.48e-1232
brain3.10e-1268
future brain3.10e-1268
cerebral hemisphere3.35e-1232
ecto-epithelium1.14e-11104
pre-chordal neural plate1.29e-1161
regional part of cerebral cortex2.21e-1122
germ layer2.57e-11560
germ layer / neural crest2.57e-11560
embryonic tissue2.57e-11560
presumptive structure2.57e-11560
germ layer / neural crest derived structure2.57e-11560
epiblast (generic)2.57e-11560
embryo3.78e-11592
nervous system4.62e-1189
multi-cellular organism6.01e-11656
embryonic structure6.32e-11564
developing anatomical structure1.28e-10581
neocortex2.21e-1020
cerebral cortex2.18e-0925
pallium2.18e-0925
structure with developmental contribution from neural crest2.43e-09132
anatomical system3.09e-08624
anatomical conduit3.58e-08240
tube4.02e-08192
anatomical group5.19e-08625
organ system subdivision5.21e-07223
organ5.66e-07503
ectoderm-derived structure8.42e-07171
ectoderm8.42e-07171
presumptive ectoderm8.42e-07171


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
RXRA#6256312.044770283480.001145262162836830.00783557386338133



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.