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Coexpression cluster:C2790: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2790_anaplastic_mesothelioma_corpus_optic_substantia_thalamus_granulosa
|full_id=C2790_anaplastic_mesothelioma_corpus_optic_substantia_thalamus_granulosa
|id=C2790
|id=C2790

Revision as of 15:34, 12 September 2012


Full id: C2790_anaplastic_mesothelioma_corpus_optic_substantia_thalamus_granulosa



Phase1 CAGE Peaks

Hg19::chr4:41216492..41216550,-p1@APBB2
Hg19::chr4:41216552..41216567,-p2@APBB2
Hg19::chr4:41216580..41216594,-p5@APBB2
Hg19::chr4:41216619..41216637,-p3@APBB2


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>

Uber Anatomy
Ontology termp-valuen
cell layer4.25e-30312
epithelium1.26e-29309
organism subdivision1.12e-27365
anatomical cluster8.02e-26286
anatomical conduit6.00e-25241
tube8.00e-24194
multi-tissue structure1.62e-21347
multi-cellular organism2.73e-18659
neural plate1.53e-1686
presumptive neural plate1.53e-1686
vasculature4.95e-1679
vascular system4.95e-1679
head4.29e-15123
brain4.44e-1569
future brain4.44e-1569
regional part of brain7.40e-1559
neural tube1.21e-1457
neural rod1.21e-1457
future spinal cord1.21e-1457
neural keel1.21e-1457
anatomical system1.45e-14625
neurectoderm1.69e-1490
anatomical group2.59e-14626
anterior region of body3.64e-14129
craniocervical region3.64e-14129
ectoderm-derived structure4.50e-14169
embryo1.04e-13612
splanchnic layer of lateral plate mesoderm1.23e-1384
embryonic structure1.98e-13605
developing anatomical structure1.98e-13605
unilaminar epithelium2.14e-13138
central nervous system2.92e-1382
germ layer3.91e-13604
embryonic tissue3.91e-13604
presumptive structure3.91e-13604
epiblast (generic)3.91e-13604
vessel4.97e-1369
trunk5.37e-13216
blood vessel7.37e-1360
epithelial tube open at both ends7.37e-1360
blood vasculature7.37e-1360
vascular cord7.37e-1360
ectoderm8.01e-13173
presumptive ectoderm8.01e-13173
regional part of nervous system9.49e-1394
nervous system9.49e-1394
epithelial tube5.67e-12118
anterior neural tube2.24e-1142
pre-chordal neural plate2.68e-1161
regional part of forebrain4.83e-1141
forebrain4.83e-1141
future forebrain4.83e-1141
artery6.96e-1142
arterial blood vessel6.96e-1142
arterial system6.96e-1142
somite1.31e-1083
paraxial mesoderm1.31e-1083
presomitic mesoderm1.31e-1083
presumptive segmental plate1.31e-1083
trunk paraxial mesoderm1.31e-1083
presumptive paraxial mesoderm1.31e-1083
trunk mesenchyme1.71e-10143
cardiovascular system3.87e-10110
telencephalon4.49e-1034
gray matter4.65e-1034
brain grey matter4.65e-1034
circulatory system5.37e-10113
dermomyotome9.77e-1070
regional part of telencephalon1.33e-0933
skeletal muscle tissue2.06e-0961
striated muscle tissue2.06e-0961
myotome2.06e-0961
muscle tissue3.29e-0963
musculature3.29e-0963
musculature of body3.29e-0963
adult organism4.61e-09115
cerebral hemisphere6.30e-0932
systemic artery2.52e-0833
systemic arterial system2.52e-0833
organ part4.88e-08219
regional part of cerebral cortex6.24e-0822
organ7.09e-08511
mesenchyme1.97e-07238


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
BRCA1#672420.18423064322386.02116732184487e-060.00017966991255033
CHD2#1106410.34402283411698.73193255208051e-050.00129263544125689
CTCF#1066445.360256373075030.001211145381643620.00819241013688331
CTCFL#140690419.74647435897446.5732084880439e-060.000193380090502202
E2F1#186944.907389214879320.001724022357361790.0106730984576472
ELF1#199744.258097958807540.003041525565781240.0161196533322149
EP300#203346.77394172622320.0004748459821442640.00434983242953818
GATA3#2625427.2365163572061.81561517799785e-066.78429458228684e-05
HEY1#2346244.040111043105710.00375304636917980.0186480998025962
JUND#372746.994663941871030.000417684217818580.00392288867129089
MXI1#460149.96157162875930.0001015224754950450.0014262719690916
MYC#460945.22228187160940.001344309395272740.00889159777915702
NR3C1#2908414.9730233311731.98868032687801e-050.000443889259796564
NRF1#4899412.21027944771094.49717228915276e-050.000795124727792154
PAX5#507946.669565531177830.0005052774169483260.00444684150574418
RAD21#5885410.35503389545638.6948481184721e-050.0012980006327117
SMC3#9126415.04493284493281.95092670935632e-050.000439217147226697
SP1#666745.69838137814090.0009482606065333980.00685413450659157
TAF1#687243.343046285745290.008005664898701650.0323044446470714
TAF7#6879411.43306940492395.85061525419808e-050.000971125884509207
TBP#690843.706770687096390.005296377814784350.0244831763200222



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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