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Coexpression cluster:C1129: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1129_mature_hippocampus_spinal_substantia_corpus_thalamus_breast
|full_id=C1129_mature_hippocampus_spinal_substantia_corpus_thalamus_breast
|gostat_on_coexpression_clusters=GO:0004621!glycosylphosphatidylinositol phospholipase D activity!0.0127157931504338!2822$GO:0032387!negative regulation of intracellular transport!0.0127157931504338!1410$GO:0004630!phospholipase D activity!0.0254270947850913!2822$GO:0030742!GTP-dependent protein binding!0.0349545369002825!22808
|gostat_on_coexpression_clusters=GO:0004621!glycosylphosphatidylinositol phospholipase D activity!0.0127157931504338!2822$GO:0032387!negative regulation of intracellular transport!0.0127157931504338!1410$GO:0004630!phospholipase D activity!0.0254270947850913!2822$GO:0030742!GTP-dependent protein binding!0.0349545369002825!22808

Revision as of 13:36, 12 September 2012


Full id: C1129_mature_hippocampus_spinal_substantia_corpus_thalamus_breast



Phase1 CAGE Peaks

Hg19::chr11:111782696..111782707,-p3@CRYAB
Hg19::chr3:138067105..138067137,+p6@MRAS
Hg19::chr3:138067461..138067488,+p3@MRAS
Hg19::chr3:138067492..138067519,+p2@MRAS
Hg19::chr3:138067521..138067553,+p5@MRAS
Hg19::chr4:2061045..2061064,+p1@NAT8L
Hg19::chr6:24495348..24495380,-p5@GPLD1


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:0004621glycosylphosphatidylinositol phospholipase D activity0.0127157931504338
GO:0032387negative regulation of intracellular transport0.0127157931504338
GO:0004630phospholipase D activity0.0254270947850913
GO:0030742GTP-dependent protein binding0.0349545369002825



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
non-terminally differentiated cell6.38e-12180
fat cell1.75e-0915
Uber Anatomy
Ontology termp-valuen
adult organism1.82e-31115
neural tube4.69e-2757
neural rod4.69e-2757
future spinal cord4.69e-2757
neural keel4.69e-2757
central nervous system1.55e-2482
regional part of brain3.02e-2359
neural plate3.28e-2386
presumptive neural plate3.28e-2386
regional part of nervous system3.92e-2394
nervous system3.92e-2394
brain1.20e-2269
future brain1.20e-2269
anterior neural tube1.89e-2042
neurectoderm4.02e-2090
organism subdivision7.61e-20365
regional part of forebrain8.68e-2041
forebrain8.68e-2041
future forebrain8.68e-2041
gray matter8.73e-1834
brain grey matter8.73e-1834
telencephalon1.11e-1734
multi-cellular organism1.26e-17659
organ2.90e-17511
regional part of telencephalon4.60e-1733
ectoderm-derived structure6.68e-17169
head1.29e-16123
cerebral hemisphere1.59e-1632
anatomical system2.29e-16625
anatomical group4.68e-16626
pre-chordal neural plate1.36e-1561
ectoderm3.55e-15173
presumptive ectoderm3.55e-15173
anterior region of body6.85e-15129
craniocervical region6.85e-15129
multi-tissue structure6.17e-14347
regional part of cerebral cortex5.06e-1322
cerebral cortex1.53e-1225
pallium1.53e-1225
neocortex8.38e-1220
embryonic structure1.15e-11605
developing anatomical structure1.15e-11605
germ layer1.54e-11604
embryonic tissue1.54e-11604
presumptive structure1.54e-11604
epiblast (generic)1.54e-11604
embryo1.64e-11612
tube3.86e-10194
epithelium1.66e-09309
anatomical conduit2.00e-09241
cell layer3.37e-09312
anatomical cluster3.73e-09286
organ part1.44e-08219
posterior neural tube9.19e-0815
chordal neural plate9.19e-0815
nucleus of brain8.30e-079
neural nucleus8.30e-079
basal ganglion8.69e-079
nuclear complex of neuraxis8.69e-079
aggregate regional part of brain8.69e-079
collection of basal ganglia8.69e-079
cerebral subcortex8.69e-079


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
CTCF#1066453.828754552196450.003387371192681340.0172901451538266
CTCFL#140690411.28369963369960.0002032736265059930.00241328797074677
E2F1#186953.505278010628090.005090553587915050.0236847830965501
E2F6#187653.583682665498130.004598101897827240.0217225839827737
EGR1#195864.275582081265830.0003762130619866450.00373562616284686
HDAC2#306647.666068706643580.0008986373447057820.0066856237101957
RAD21#588557.39645278246880.0001491014505228370.00192294472600081
SMARCB1#6598410.43012330351850.0002755863833009370.00293603654856336
TCF7L2#693446.154386607507050.002064676148138040.0119696204404878
TFAP2A#702037.079414731304980.006452554472180970.028027713214112
TFAP2C#702246.176702062777270.002036754928069020.0118274477582764
ZBTB7A#5134155.251363791339930.0007687692483214460.00603000311869647



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.