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Coexpression cluster:C485: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.359196,0.132539,1.71024,0.19904,0.287896,0.197892,0.253108,0.926519,1.31362,1.32587,0.177199,0.286323,1.45083,1.2694,0.0842592,0.65729,0.43322,0.468601,1.54367,0.320781,0.107335,2.25678,0.192508,0.0823774,0.827313,0.304148,0.194566,1.0629,0.0865304,0.844228,0.162709,0.465029,0.174335,0.72907,0.885147,0.0638435,0.0667305,1.09331,0.0564451,0.117466,0.0675531,0.152186,2.89429,0.283867,2.71105,1.86356,0.253928,0.507207,2.73445,1.51874,0.315441,1.33789,0.108424,1.31921,0.671855,0.246686,0.0887806,0.633499,1.18142,0.221865,0.500944,0.710665,1.31661,1.05455,1.36195,0.380605,0.754286,1.10771,0.456006,0.950487,0.143869,1.36375,0.105378,0.670004,0.224282,0.201182,3.63084,0.395294,0.45319,1.31673,0.266362,1.05257,0.269087,0.330114,0.622646,0.118932,0.0781398,0.0595657,0.336397,1.20481,0.84263,0.598,0.4797,0.0486298,0.0853298,0.0539379,0.103727,0.517267,0.340143,0.00964183,0.208183,0.474756,0.512318,0.436368,2.59571,0.174162,0.422802,1.25974,1.33917,0.0770225,1.76613,0.509866,0.104228,0.183573,0.797061,1.82027,0.265834,0.161925,0.378653,0.0497592,0.662347,0.334429,0.195973,0.277756,0.90249,0.395934,0.248345,0.484077,0.701879,0.771918,0.598629,0.164582,0.715286,0.275188,0.854902,0.0111458,0.158817,0.191402,0.814541,1.65405,1.25623,0.779227,1.28869,0.514137,0.372477,0.216494,0.35869,1.49614,3.53535,0.178999,0.354858,0.192274,0.598976,0.30216,0.255347,0.980005,0.32333,0.0779979,0.417768,0.116987,0.77808,0.582159,0.452507,0.378488,0.385896,0.268483,0.16475,0.252107,2.46113
}}
}}

Revision as of 14:15, 26 November 2012


Full id: C485_Pericytes_retina_cerebral_Dendritic_testis_corpus_spinal



Phase1 CAGE Peaks

Hg19::chr9:139871948..139871964,+p1@PTGDS
Hg19::chr9:139873437..139873444,+p14@PTGDS
Hg19::chr9:139873445..139873481,+p2@PTGDS
Hg19::chr9:139873495..139873543,+p3@PTGDS
Hg19::chr9:139873544..139873562,+p9@PTGDS
Hg19::chr9:139873670..139873734,+p@chr9:139873670..139873734
+
Hg19::chr9:139874396..139874457,+p4@PTGDS
Hg19::chr9:139874436..139874463,-p@chr9:139874436..139874463
-
Hg19::chr9:139874466..139874495,+p8@PTGDS
Hg19::chr9:139874472..139874481,-p@chr9:139874472..139874481
-
Hg19::chr9:139874503..139874516,-p@chr9:139874503..139874516
-
Hg19::chr9:139874630..139874648,+p11@PTGDS
Hg19::chr9:139874657..139874682,-p@chr9:139874657..139874682
-
Hg19::chr9:139874662..139874682,+p10@PTGDS
Hg19::chr9:139874683..139874714,+p5@PTGDS
Hg19::chr9:139874710..139874744,-p@chr9:139874710..139874744
-
Hg19::chr9:139875304..139875308,-p@chr9:139875304..139875308
-
Hg19::chr9:139876037..139876053,+p3@LCNL1
Hg19::chr9:139876097..139876149,-p@chr9:139876097..139876149
-
Hg19::chr9:139876112..139876142,+p2@LCNL1


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:0022410circadian sleep/wake cycle process0.000485694101024373
GO:0042749regulation of circadian sleep/wake cycle0.000485694101024373
GO:0045187regulation of circadian sleep/wake cycle, sleep0.000485694101024373
GO:0050802circadian sleep/wake cycle, sleep0.000485694101024373
GO:0042745circadian sleep/wake cycle0.000647592134699163
GO:0004667prostaglandin-D synthase activity0.000647592134699163
GO:0048512circadian behavior0.000647592134699163
GO:0007622rhythmic behavior0.000647592134699163
GO:0042752regulation of circadian rhythm0.000647592134699163
GO:0030431sleep0.000971388202048745
GO:0046457prostanoid biosynthetic process0.00161898033674791
GO:0001516prostaglandin biosynthetic process0.00161898033674791
GO:0005791rough endoplasmic reticulum0.00194277640409749
GO:0006693prostaglandin metabolic process0.00194277640409749
GO:0006692prostanoid metabolic process0.00194277640409749
GO:0019840isoprenoid binding0.00194277640409749
GO:0005501retinoid binding0.00194277640409749
GO:0007623circadian rhythm0.00313002865104596
GO:0046456icosanoid biosynthetic process0.00337429585974827
GO:0006690icosanoid metabolic process0.00485694101024373
GO:0016860intramolecular oxidoreductase activity0.00638340818489176
GO:0006633fatty acid biosynthetic process0.00644648534086895
GO:0016053organic acid biosynthetic process0.00671876839750383
GO:0046394carboxylic acid biosynthetic process0.00671876839750383
GO:0031965nuclear membrane0.0117343694807488
GO:0006631fatty acid metabolic process0.0139592082368486
GO:0005635nuclear envelope0.0139592082368486
GO:0051239regulation of multicellular organismal process0.0190392087601554
GO:0032787monocarboxylic acid metabolic process0.0190392087601554
GO:0007610behavior0.0190392087601554
GO:0016853isomerase activity0.0196784448673101
GO:0008610lipid biosynthetic process0.0202170169551395
GO:0031967organelle envelope0.0356556610634363
GO:0031975envelope0.0356556610634363
GO:0005794Golgi apparatus0.0385779885956502
GO:0044255cellular lipid metabolic process0.0407983044860473
GO:0019752carboxylic acid metabolic process0.0407983044860473
GO:0006082organic acid metabolic process0.0407983044860473
GO:0005783endoplasmic reticulum0.0451321903105725
GO:0006629lipid metabolic process0.0459466619569057
GO:0012505endomembrane system0.0487115644734688



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.08e-71114
neural tube2.00e-4456
neural rod2.00e-4456
future spinal cord2.00e-4456
neural keel2.00e-4456
regional part of nervous system6.99e-4153
regional part of brain6.99e-4153
brain5.16e-3968
future brain5.16e-3968
central nervous system3.22e-3881
neural plate9.18e-3882
presumptive neural plate9.18e-3882
neurectoderm2.97e-3686
regional part of forebrain1.22e-3441
forebrain1.22e-3441
anterior neural tube1.22e-3441
future forebrain1.22e-3441
nervous system5.36e-3489
brain grey matter1.67e-2934
gray matter1.67e-2934
telencephalon1.69e-2934
ecto-epithelium8.04e-29104
regional part of telencephalon2.08e-2732
pre-chordal neural plate2.81e-2761
cerebral hemisphere3.76e-2732
structure with developmental contribution from neural crest7.31e-25132
regional part of cerebral cortex1.18e-2322
neocortex1.49e-2120
ectoderm-derived structure2.03e-21171
ectoderm2.03e-21171
presumptive ectoderm2.03e-21171
cerebral cortex5.90e-2025
pallium5.90e-2025
organ system subdivision2.36e-17223
organ part1.96e-15218
organ1.28e-13503
multi-tissue structure7.07e-13342
epithelium5.38e-12306
cell layer1.27e-11309
neural nucleus3.44e-119
nucleus of brain3.44e-119
basal ganglion3.88e-119
nuclear complex of neuraxis3.88e-119
aggregate regional part of brain3.88e-119
collection of basal ganglia3.88e-119
cerebral subcortex3.88e-119
anatomical cluster4.72e-11373
posterior neural tube9.50e-1115
chordal neural plate9.50e-1115
germ layer1.07e-10560
germ layer / neural crest1.07e-10560
embryonic tissue1.07e-10560
presumptive structure1.07e-10560
germ layer / neural crest derived structure1.07e-10560
epiblast (generic)1.07e-10560
embryonic structure2.44e-10564
multi-cellular organism3.23e-10656
tube1.06e-09192
developing anatomical structure1.24e-09581
embryo3.16e-09592
telencephalic nucleus3.95e-097
anatomical conduit4.85e-09240
anatomical system7.12e-09624
anatomical group8.57e-09625
segmental subdivision of nervous system1.05e-0813
temporal lobe2.12e-086
brainstem8.00e-086
segmental subdivision of hindbrain1.37e-0712
hindbrain1.37e-0712
presumptive hindbrain1.37e-0712
gyrus2.04e-076


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

No analysis results for this cluster

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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