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Coexpression cluster:C4748: Difference between revisions

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|tf_chipseq_enrich=NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000741591045881708!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191269951619053!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00423344224122173
|tf_chipseq_enrich=NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000741591045881708!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191269951619053!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00423344224122173
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}}
}}

Revision as of 16:56, 26 November 2012


Full id: C4748_parietal_occipital_brain_Neurons_temporal_small_duodenum



Phase1 CAGE Peaks

Hg19::chr8:35092959..35092973,+p2@UNC5D
Hg19::chr8:35092985..35093003,+p1@UNC5D
Hg19::chr8:35093006..35093017,+p3@UNC5D


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
neuronal stem cell5.38e-148
neuron4.12e-116
neuroblast4.12e-116
electrically signaling cell4.12e-116
embryonic stem cell9.65e-085
neural cell4.83e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system7.27e-7081
nervous system4.99e-6789
neural tube1.10e-5656
neural rod1.10e-5656
future spinal cord1.10e-5656
neural keel1.10e-5656
regional part of nervous system2.68e-5353
regional part of brain2.68e-5353
brain7.13e-5268
future brain7.13e-5268
neurectoderm2.32e-5086
neural plate6.22e-5082
presumptive neural plate6.22e-5082
regional part of forebrain1.35e-4641
forebrain1.35e-4641
anterior neural tube1.35e-4641
future forebrain1.35e-4641
pre-chordal neural plate1.70e-4461
ectoderm-derived structure1.15e-43171
ectoderm1.15e-43171
presumptive ectoderm1.15e-43171
cerebral hemisphere1.69e-3832
ecto-epithelium2.21e-38104
brain grey matter3.10e-3834
gray matter3.10e-3834
telencephalon5.48e-3834
regional part of telencephalon1.18e-3532
regional part of cerebral cortex5.12e-3222
cerebral cortex1.15e-2925
pallium1.15e-2925
neocortex3.38e-2920
organ system subdivision4.88e-29223
structure with developmental contribution from neural crest1.08e-28132
adult organism1.41e-28114
anatomical cluster3.38e-18373
posterior neural tube2.70e-1115
chordal neural plate2.70e-1115
basal ganglion2.95e-109
nuclear complex of neuraxis2.95e-109
aggregate regional part of brain2.95e-109
collection of basal ganglia2.95e-109
cerebral subcortex2.95e-109
gyrus3.65e-106
embryo5.10e-10592
neural nucleus6.20e-109
nucleus of brain6.20e-109
organ part6.77e-10218
diencephalon6.94e-107
future diencephalon6.94e-107
tube2.12e-09192
parietal lobe4.34e-095
occipital lobe5.98e-095
temporal lobe8.18e-096
limbic system1.32e-085
segmental subdivision of hindbrain2.49e-0812
hindbrain2.49e-0812
presumptive hindbrain2.49e-0812
multi-cellular organism3.17e-08656
multi-tissue structure5.15e-08342
segmental subdivision of nervous system1.53e-0713
telencephalic nucleus1.77e-077
pigment epithelium of eye2.08e-0711
developing anatomical structure2.20e-07581
regional part of metencephalon3.49e-079
metencephalon3.49e-079
future metencephalon3.49e-079
embryonic structure3.71e-07564
germ layer5.21e-07560
germ layer / neural crest5.21e-07560
embryonic tissue5.21e-07560
presumptive structure5.21e-07560
germ layer / neural crest derived structure5.21e-07560
epiblast (generic)5.21e-07560
atypical epithelium6.08e-074
corpus striatum6.17e-074
striatum6.17e-074
ventral part of telencephalon6.17e-074
future corpus striatum6.17e-074
gland of diencephalon7.42e-074
neuroendocrine gland7.42e-074
organ9.23e-07503


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
NANOG#79923329.24477848101273.99627955670032e-050.000741591045881708
USF1#739136.361499277207960.00388404057290560.0191269951619053
USF2#7392312.99219738506960.0004558979393427810.00423344224122173



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.

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