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Coexpression cluster:C1482

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Full id: C1482_caudate_anaplastic_putamen_thalamus_small_diencephalon_nucleus



Phase1 CAGE Peaks

Hg19::chr20:60795296..60795309,-p2@HRH3
Hg19::chr20:60795316..60795323,-p3@HRH3
Hg19::chr20:60795326..60795340,-p1@HRH3
Hg19::chr2:242089628..242089643,-p5@PASK
Hg19::chr3:58810185..58810229,+p1@ENST00000463703
p1@ENST00000482372
p1@uc003dku.1
Hg19::chr4:72102152..72102166,+p16@SLC4A4


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:0008510sodium:bicarbonate symporter activity0.0323188318986822
GO:0004969histamine receptor activity0.0475105037576734
GO:0015106bicarbonate transmembrane transporter activity0.0475105037576734
GO:0005452inorganic anion exchanger activity0.0475105037576734
GO:0015380anion exchanger activity0.0475105037576734
GO:0015301anion:anion antiporter activity0.0475105037576734
GO:0015108chloride transmembrane transporter activity0.0475105037576734
GO:0015296anion:cation symporter activity0.0475105037576734
GO:0007269neurotransmitter secretion0.0475105037576734
GO:0005887integral to plasma membrane0.0475105037576734
GO:0031226intrinsic to plasma membrane0.0475105037576734
GO:0045055regulated secretory pathway0.0475105037576734



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
embryonic stem cell1.74e-075
Uber Anatomy
Ontology termp-valuen
neural tube8.76e-8056
neural rod8.76e-8056
future spinal cord8.76e-8056
neural keel8.76e-8056
regional part of nervous system1.97e-7353
regional part of brain1.97e-7353
nervous system6.51e-7189
central nervous system1.12e-7081
brain2.79e-6368
future brain2.79e-6368
regional part of forebrain2.87e-6241
forebrain2.87e-6241
anterior neural tube2.87e-6241
future forebrain2.87e-6241
telencephalon4.00e-6234
brain grey matter4.47e-6234
gray matter4.47e-6234
cerebral hemisphere4.76e-6232
regional part of telencephalon1.57e-5732
neural plate4.82e-5682
presumptive neural plate4.82e-5682
neurectoderm7.35e-5386
regional part of cerebral cortex6.49e-5122
neocortex3.71e-4620
ecto-epithelium8.83e-46104
cerebral cortex2.87e-4425
pallium2.87e-4425
pre-chordal neural plate3.21e-4461
adult organism4.64e-39114
ectoderm-derived structure5.62e-35171
ectoderm5.62e-35171
presumptive ectoderm5.62e-35171
structure with developmental contribution from neural crest7.45e-35132
organ system subdivision6.74e-28223
tube1.02e-19192
basal ganglion2.29e-199
nuclear complex of neuraxis2.29e-199
aggregate regional part of brain2.29e-199
collection of basal ganglia2.29e-199
cerebral subcortex2.29e-199
neural nucleus6.24e-199
nucleus of brain6.24e-199
posterior neural tube6.78e-1815
chordal neural plate6.78e-1815
gyrus5.44e-166
telencephalic nucleus1.59e-147
anatomical conduit4.83e-14240
limbic system6.86e-145
temporal lobe2.18e-136
anatomical cluster2.33e-13373
parietal lobe3.49e-135
occipital lobe4.28e-135
segmental subdivision of hindbrain2.62e-1212
hindbrain2.62e-1212
presumptive hindbrain2.62e-1212
epithelium2.69e-12306
corpus striatum3.35e-124
striatum3.35e-124
ventral part of telencephalon3.35e-124
future corpus striatum3.35e-124
cell layer4.81e-12309
organ part1.84e-11218
segmental subdivision of nervous system3.01e-1113
brainstem2.32e-106
regional part of metencephalon1.02e-099
metencephalon1.02e-099
future metencephalon1.02e-099
caudate-putamen1.40e-093
dorsal striatum1.40e-093
frontal cortex4.59e-093
pons3.02e-083
spinal cord8.30e-083
dorsal region element8.30e-083
dorsum8.30e-083
embryo1.15e-07592
multi-tissue structure2.64e-07342
caudate nucleus6.27e-072
future caudate nucleus6.27e-072
dorsal plus ventral thalamus9.22e-072
thalamic complex9.22e-072


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
ETS1#211346.485840614801560.001410474068463220.00917067180702423
HDAC2#306636.707810118313130.006973940027962660.0294902956749693
SIN3A#2594243.605923151210090.01273893844487140.0459470228016273



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.