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Coexpression cluster:C2754

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Full id: C2754_temporal_duodenum_nonsmall_occipital_parietal_Nucleus_putamen



Phase1 CAGE Peaks

Hg19::chr3:79817111..79817121,-p11@ROBO1
Hg19::chr3:79817136..79817155,-p4@ROBO1
Hg19::chr3:79817162..79817175,-p6@ROBO1
Hg19::chr3:79817277..79817296,-p9@ROBO1


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
regional part of nervous system2.58e-5294
nervous system2.58e-5294
central nervous system9.46e-5282
regional part of brain7.27e-4959
neural tube2.24e-4657
neural rod2.24e-4657
future spinal cord2.24e-4657
neural keel2.24e-4657
brain2.66e-4369
future brain2.66e-4369
neurectoderm4.07e-4390
neural plate4.77e-4386
presumptive neural plate4.77e-4386
regional part of forebrain4.41e-3741
forebrain4.41e-3741
future forebrain4.41e-3741
anterior neural tube7.27e-3642
pre-chordal neural plate3.60e-3561
gray matter7.76e-3334
brain grey matter7.76e-3334
telencephalon3.52e-3234
regional part of telencephalon3.50e-3133
cerebral hemisphere5.44e-3132
anterior region of body3.95e-30129
craniocervical region3.95e-30129
ectoderm8.88e-30173
presumptive ectoderm8.88e-30173
ectoderm-derived structure3.38e-29169
head2.24e-28123
adult organism1.74e-24115
cerebral cortex1.97e-2325
pallium1.97e-2325
regional part of cerebral cortex1.51e-2122
neocortex2.74e-1920
multi-tissue structure1.80e-11347
anatomical cluster2.00e-11286
posterior neural tube2.23e-1115
chordal neural plate2.23e-1115
cell layer2.28e-11312
nucleus of brain7.76e-119
neural nucleus7.76e-119
epithelium8.51e-11309
basal ganglion9.06e-119
nuclear complex of neuraxis9.06e-119
aggregate regional part of brain9.06e-119
collection of basal ganglia9.06e-119
cerebral subcortex9.06e-119
temporal lobe1.67e-097
tube1.68e-09194
organism subdivision6.41e-09365
embryo9.22e-09612
telencephalic nucleus1.67e-087
segmental subdivision of hindbrain2.66e-0812
hindbrain2.66e-0812
presumptive hindbrain2.66e-0812
vasculature of head5.67e-0811
vasculature of organ5.67e-0811
multi-cellular organism6.09e-08659
organ part9.69e-08219
embryonic structure1.22e-07605
developing anatomical structure1.22e-07605
anatomical conduit1.28e-07241
segmental subdivision of nervous system1.84e-0713
limbic system2.31e-075
brain vasculature2.55e-075
dorsal region element2.59e-075
dorsum2.59e-075
germ layer2.86e-07604
embryonic tissue2.86e-07604
presumptive structure2.86e-07604
epiblast (generic)2.86e-07604
brainstem5.48e-078


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
USF1#739146.361499277207960.0006105011399140830.00508697371561249



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.