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Coexpression cluster:C1142: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!4.24e-36!365;UBERON:0000119!6.08e-33!312;UBERON:0000483!1.23e-31!309;UBERON:0000481!2.70e-26!347;UBERON:0000477!5.15e-24!286;UBERON:0000468!3.81e-22!659;UBERON:0000025!6.31e-22!194;UBERON:0000914!2.10e-21!83;UBERON:0002329!2.10e-21!83;UBERON:0003077!2.10e-21!83;UBERON:0003059!2.10e-21!83;UBERON:0007282!2.10e-21!83;UBERON:0009618!2.10e-21!83;UBERON:0007285!2.10e-21!83;UBERON:0004111!1.24e-20!241;UBERON:0004290!3.85e-19!70;UBERON:0005256!1.05e-18!143;UBERON:0000486!1.00e-17!82;UBERON:0000467!1.45e-17!625;UBERON:0001134!1.88e-17!61;UBERON:0002036!1.88e-17!61;UBERON:0003082!1.88e-17!61;UBERON:0000480!3.63e-17!626;UBERON:0002385!1.11e-16!63;UBERON:0001015!1.11e-16!63;UBERON:0000383!1.11e-16!63;UBERON:0000033!2.52e-16!123;UBERON:0004121!5.48e-16!169;UBERON:0000922!6.78e-16!612;UBERON:0002050!1.26e-15!605;UBERON:0005423!1.26e-15!605;UBERON:0000923!1.66e-15!604;UBERON:0005291!1.66e-15!604;UBERON:0006598!1.66e-15!604;UBERON:0002532!1.66e-15!604;UBERON:0000924!3.68e-15!173;UBERON:0006601!3.68e-15!173;UBERON:0003075!4.59e-15!86;UBERON:0007284!4.59e-15!86;UBERON:0002049!6.22e-15!79;UBERON:0007798!6.22e-15!79;UBERON:0002100!1.21e-14!216;UBERON:0005743!2.52e-14!86;UBERON:0000153!3.47e-14!129;UBERON:0007811!3.47e-14!129;UBERON:0000064!4.14e-14!219;UBERON:0000955!6.49e-14!69;UBERON:0006238!6.49e-14!69;UBERON:0004872!7.70e-14!84;UBERON:0002346!8.14e-14!90;UBERON:0001017!9.86e-14!82;UBERON:0002616!1.22e-13!59;UBERON:0003914!4.87e-13!118;UBERON:0003056!5.46e-13!61;UBERON:0000073!5.82e-13!94;UBERON:0001016!5.82e-13!94;UBERON:0001049!2.55e-12!57;UBERON:0005068!2.55e-12!57;UBERON:0006241!2.55e-12!57;UBERON:0007135!2.55e-12!57;UBERON:0001981!1.37e-11!60;UBERON:0007500!1.37e-11!60;UBERON:0004537!1.37e-11!60;UBERON:0006965!1.37e-11!60;UBERON:0000055!2.50e-11!69;UBERON:0001637!4.55e-11!42;UBERON:0003509!4.55e-11!42;UBERON:0004572!4.55e-11!42;UBERON:0000490!1.19e-10!138;UBERON:0001009!3.05e-10!113;UBERON:0004535!3.39e-10!110;UBERON:0002780!5.18e-10!41;UBERON:0001890!5.18e-10!41;UBERON:0006240!5.18e-10!41;UBERON:0003080!1.17e-09!42;UBERON:0001893!1.76e-09!34;UBERON:0003104!2.00e-09!238;UBERON:0009142!2.00e-09!238;UBERON:0001869!3.24e-09!32;UBERON:0002791!5.36e-09!33;UBERON:0002020!9.70e-09!34;UBERON:0003528!9.70e-09!34;UBERON:0004573!1.07e-08!33;UBERON:0004571!1.07e-08!33;UBERON:0000956!1.92e-07!25;UBERON:0000203!1.92e-07!25;UBERON:0002619!2.95e-07!22;UBERON:0001950!5.43e-07!20;UBERON:0000062!9.16e-07!511
|ontology_enrichment_uberon=UBERON:0000475!4.24e-36!365;UBERON:0000119!6.08e-33!312;UBERON:0000483!1.23e-31!309;UBERON:0000481!2.70e-26!347;UBERON:0000477!5.15e-24!286;UBERON:0000468!3.81e-22!659;UBERON:0000025!6.31e-22!194;UBERON:0000914!2.10e-21!83;UBERON:0002329!2.10e-21!83;UBERON:0003077!2.10e-21!83;UBERON:0003059!2.10e-21!83;UBERON:0007282!2.10e-21!83;UBERON:0009618!2.10e-21!83;UBERON:0007285!2.10e-21!83;UBERON:0004111!1.24e-20!241;UBERON:0004290!3.85e-19!70;UBERON:0005256!1.05e-18!143;UBERON:0000486!1.00e-17!82;UBERON:0000467!1.45e-17!625;UBERON:0001134!1.88e-17!61;UBERON:0002036!1.88e-17!61;UBERON:0003082!1.88e-17!61;UBERON:0000480!3.63e-17!626;UBERON:0002385!1.11e-16!63;UBERON:0001015!1.11e-16!63;UBERON:0000383!1.11e-16!63;UBERON:0000033!2.52e-16!123;UBERON:0004121!5.48e-16!169;UBERON:0000922!6.78e-16!612;UBERON:0002050!1.26e-15!605;UBERON:0005423!1.26e-15!605;UBERON:0000923!1.66e-15!604;UBERON:0005291!1.66e-15!604;UBERON:0006598!1.66e-15!604;UBERON:0002532!1.66e-15!604;UBERON:0000924!3.68e-15!173;UBERON:0006601!3.68e-15!173;UBERON:0003075!4.59e-15!86;UBERON:0007284!4.59e-15!86;UBERON:0002049!6.22e-15!79;UBERON:0007798!6.22e-15!79;UBERON:0002100!1.21e-14!216;UBERON:0005743!2.52e-14!86;UBERON:0000153!3.47e-14!129;UBERON:0007811!3.47e-14!129;UBERON:0000064!4.14e-14!219;UBERON:0000955!6.49e-14!69;UBERON:0006238!6.49e-14!69;UBERON:0004872!7.70e-14!84;UBERON:0002346!8.14e-14!90;UBERON:0001017!9.86e-14!82;UBERON:0002616!1.22e-13!59;UBERON:0003914!4.87e-13!118;UBERON:0003056!5.46e-13!61;UBERON:0000073!5.82e-13!94;UBERON:0001016!5.82e-13!94;UBERON:0001049!2.55e-12!57;UBERON:0005068!2.55e-12!57;UBERON:0006241!2.55e-12!57;UBERON:0007135!2.55e-12!57;UBERON:0001981!1.37e-11!60;UBERON:0007500!1.37e-11!60;UBERON:0004537!1.37e-11!60;UBERON:0006965!1.37e-11!60;UBERON:0000055!2.50e-11!69;UBERON:0001637!4.55e-11!42;UBERON:0003509!4.55e-11!42;UBERON:0004572!4.55e-11!42;UBERON:0000490!1.19e-10!138;UBERON:0001009!3.05e-10!113;UBERON:0004535!3.39e-10!110;UBERON:0002780!5.18e-10!41;UBERON:0001890!5.18e-10!41;UBERON:0006240!5.18e-10!41;UBERON:0003080!1.17e-09!42;UBERON:0001893!1.76e-09!34;UBERON:0003104!2.00e-09!238;UBERON:0009142!2.00e-09!238;UBERON:0001869!3.24e-09!32;UBERON:0002791!5.36e-09!33;UBERON:0002020!9.70e-09!34;UBERON:0003528!9.70e-09!34;UBERON:0004573!1.07e-08!33;UBERON:0004571!1.07e-08!33;UBERON:0000956!1.92e-07!25;UBERON:0000203!1.92e-07!25;UBERON:0002619!2.95e-07!22;UBERON:0001950!5.43e-07!20;UBERON:0000062!9.16e-07!511
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}}
}}

Revision as of 12:14, 5 September 2012


Full id: C1142_Mesenchymal_Fibroblast_Pericytes_Smooth_Renal_Hepatic_Hair



Phase1 CAGE Peaks

Hg19::chr11:46958264..46958342,+p1@C11orf49
Hg19::chr20:327736..327767,+p1@NRSN2
Hg19::chr2:27545939..27545981,-p1@MPV17
Hg19::chrX:134156502..134156577,-p1@FAM127C
Hg19::chrX:134166360..134166371,+p2@FAM127A
Hg19::chrX:134166376..134166394,+p1@FAM127A
Hg19::chrX:48931650..48931681,-p1@PRAF2


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:0000002mitochondrial genome maintenance0.0240980092024216
GO:0015813L-glutamate transport0.0240980092024216
GO:0015800acidic amino acid transport0.0240980092024216
GO:0005779integral to peroxisomal membrane0.0240980092024216
GO:0031231intrinsic to peroxisomal membrane0.0240980092024216
GO:0043025cell soma0.0321322983860711
GO:0031903microbody membrane0.0321322983860711
GO:0006800oxygen and reactive oxygen species metabolic process0.0321322983860711
GO:0005778peroxisomal membrane0.0321322983860711
GO:0044439peroxisomal part0.0321322983860711
GO:0044438microbody part0.0321322983860711
GO:0016020membrane0.036124967424513
GO:0030133transport vesicle0.0364189068602428
GO:0006865amino acid transport0.0375136993092468
GO:0015837amine transport0.0375136993092468
GO:0007005mitochondrion organization and biogenesis0.0375136993092468
GO:0046942carboxylic acid transport0.0375136993092468
GO:0015849organic acid transport0.0375136993092468
GO:0042579microbody0.0375136993092468
GO:0005777peroxisome0.0375136993092468
GO:0031301integral to organelle membrane0.0495754959062544



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
organism subdivision4.24e-36365
cell layer6.08e-33312
epithelium1.23e-31309
multi-tissue structure2.70e-26347
anatomical cluster5.15e-24286
multi-cellular organism3.81e-22659
tube6.31e-22194
somite2.10e-2183
paraxial mesoderm2.10e-2183
presomitic mesoderm2.10e-2183
presumptive segmental plate2.10e-2183
trunk paraxial mesoderm2.10e-2183
presumptive paraxial mesoderm2.10e-2183
anatomical conduit1.24e-20241
dermomyotome3.85e-1970
trunk mesenchyme1.05e-18143
multilaminar epithelium1.00e-1782
anatomical system1.45e-17625
skeletal muscle tissue1.88e-1761
striated muscle tissue1.88e-1761
myotome1.88e-1761
anatomical group3.63e-17626
muscle tissue1.11e-1663
musculature1.11e-1663
musculature of body1.11e-1663
head2.52e-16123
ectoderm-derived structure5.48e-16169
embryo6.78e-16612
embryonic structure1.26e-15605
developing anatomical structure1.26e-15605
germ layer1.66e-15604
embryonic tissue1.66e-15604
presumptive structure1.66e-15604
epiblast (generic)1.66e-15604
ectoderm3.68e-15173
presumptive ectoderm3.68e-15173
neural plate4.59e-1586
presumptive neural plate4.59e-1586
vasculature6.22e-1579
vascular system6.22e-1579
trunk1.21e-14216
anterior region of body3.47e-14129
craniocervical region3.47e-14129
organ part4.14e-14219
brain6.49e-1469
future brain6.49e-1469
splanchnic layer of lateral plate mesoderm7.70e-1484
neurectoderm8.14e-1490
central nervous system9.86e-1482
regional part of brain1.22e-1359
epithelial tube4.87e-13118
pre-chordal neural plate5.46e-1361
regional part of nervous system5.82e-1394
nervous system5.82e-1394
neural tube2.55e-1257
neural rod2.55e-1257
future spinal cord2.55e-1257
neural keel2.55e-1257
blood vessel1.37e-1160
epithelial tube open at both ends1.37e-1160
blood vasculature1.37e-1160
vascular cord1.37e-1160
vessel2.50e-1169
artery4.55e-1142
arterial blood vessel4.55e-1142
arterial system4.55e-1142
unilaminar epithelium1.19e-10138
circulatory system3.05e-10113
cardiovascular system3.39e-10110
regional part of forebrain5.18e-1041
forebrain5.18e-1041
future forebrain5.18e-1041
anterior neural tube1.17e-0942
telencephalon1.76e-0934
mesenchyme2.00e-09238
entire embryonic mesenchyme2.00e-09238
cerebral hemisphere3.24e-0932
regional part of telencephalon5.36e-0933
gray matter9.70e-0934
brain grey matter9.70e-0934
systemic artery1.07e-0833
systemic arterial system1.07e-0833
cerebral cortex1.92e-0725


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
E2F6#187653.583682665498130.004598101897827240.0217235666383416
ELF1#199753.041498542005380.009719562269370750.0365591501783048
ELK4#200536.958149282200580.006773584590600160.0287513270090506
ETS1#211345.559291955544190.003022564475303460.0160484804898942
GABPB1#255355.048345597272980.0009267438350018040.00673637245154186
HEY1#2346252.885793602218360.01231366941853030.0446211901183818
MYC#460953.730201336863860.003821944222306690.0188683541779006
POLR2A#543072.147453176558070.004747636447610280.0223260121100441
SIX5#14791237.322878009482430.00586667625269160.0263304598691387
SREBF1#6720213.43024269728240.008849476021677450.0335900572861338
TAF1#687262.865468244924540.003728330207471460.0185836433225844
USF1#739154.543928055148540.001522788355968760.00970279379592589
YY1#752853.507979107038470.005072570672808980.0236116329499264
ZNF143#770235.786089950954810.0113300558873240.0415513626945795



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.