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Coexpression cluster:C1260

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Full id: C1260_neuroectodermal_parietal_occipital_insula_amygdala_extraskeletal_frontal



Phase1 CAGE Peaks

Hg19::chr21:42218936..42218945,-p6@DSCAM
Hg19::chr21:42219044..42219059,-p4@DSCAM
Hg19::chr21:42219067..42219099,-p1@DSCAM
Hg19::chr21:42219120..42219129,-p10@DSCAM
Hg19::chr21:42219138..42219161,-p3@DSCAM
Hg19::chr21:42219168..42219187,-p2@DSCAM
Hg19::chr21:42219196..42219210,-p5@DSCAM


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
ecto-epithelial cell2.64e-1033
general ecto-epithelial cell2.72e-0913
ectodermal cell2.37e-0871
Uber Anatomy
Ontology termp-valuen
neural tube7.24e-4457
neural rod7.24e-4457
future spinal cord7.24e-4457
neural keel7.24e-4457
central nervous system9.08e-4382
regional part of nervous system1.03e-4194
nervous system1.03e-4194
regional part of forebrain1.49e-3741
forebrain1.49e-3741
future forebrain1.49e-3741
ectoderm4.81e-37173
presumptive ectoderm4.81e-37173
anterior neural tube2.91e-3642
regional part of brain9.49e-3659
brain1.88e-3569
future brain1.88e-3569
ectoderm-derived structure2.52e-35169
neurectoderm5.15e-3590
neural plate2.48e-3386
presumptive neural plate2.48e-3386
telencephalon2.44e-3134
gray matter3.47e-3134
brain grey matter3.47e-3134
regional part of telencephalon3.15e-3033
pre-chordal neural plate9.00e-3061
cerebral hemisphere2.26e-2932
head2.50e-29123
anterior region of body2.65e-29129
craniocervical region2.65e-29129
regional part of cerebral cortex4.33e-2522
neocortex3.64e-2320
cerebral cortex1.40e-2225
pallium1.40e-2225
adult organism1.21e-20115
organ part2.55e-15219
organism subdivision2.03e-13365
epithelium2.59e-10309
basal ganglion4.36e-109
nuclear complex of neuraxis4.36e-109
aggregate regional part of brain4.36e-109
collection of basal ganglia4.36e-109
cerebral subcortex4.36e-109
nucleus of brain5.06e-109
neural nucleus5.06e-109
cell layer6.18e-10312
organ1.36e-09511
temporal lobe1.66e-097
multi-cellular organism2.56e-09659
posterior neural tube6.64e-0915
chordal neural plate6.64e-0915
anatomical system6.82e-09625
anatomical group8.47e-09626
telencephalic nucleus4.22e-087
embryo4.39e-08612
gyrus6.26e-086
diencephalon1.52e-077
future diencephalon1.52e-077
segmental subdivision of nervous system3.36e-0713
germ layer4.56e-07604
embryonic tissue4.56e-07604
presumptive structure4.56e-07604
epiblast (generic)4.56e-07604
tube4.66e-07194
embryonic structure5.53e-07605
developing anatomical structure5.53e-07605
parietal lobe7.47e-075
brainstem7.75e-078
occipital lobe7.99e-075


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
REST#597879.650028716128021.28195528172884e-077.32418641512461e-06
SUZ12#23512750.11578091106291.25242994278099e-121.74636222689057e-10
TBP#690873.706770687096390.0001039672097505110.00145182931128943
USF1#739176.361499277207962.37038582734158e-068.40613668664607e-05



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.