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Coexpression cluster:C333: Difference between revisions

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|full_id=C333_Fibroblast_Smooth_Preadipocyte_Adipocyte_Ewing_Placental_sacrococcigeal
|full_id=C333_Fibroblast_Smooth_Preadipocyte_Adipocyte_Ewing_Placental_sacrococcigeal
|id=C333
|id=C333
|ontology_enrichment_celltype=CL:0000055!8.24e-34!180;CL:0000057!4.60e-19!75;CL:0000680!2.81e-17!57;CL:0000056!2.81e-17!57;CL:0000355!2.81e-17!57;CL:0000187!5.28e-16!54;CL:0000183!2.16e-14!59;CL:0000192!8.08e-13!42;CL:0000514!8.08e-13!42;CL:0000393!1.00e-12!60;CL:0000211!1.00e-12!60;CL:0000222!4.54e-12!119;CL:0000359!1.35e-10!32;CL:0002620!5.54e-09!23;CL:0000136!3.90e-08!15;CL:0002334!1.85e-07!12;CL:0000220!4.34e-07!246;CL:0002494!5.44e-07!16;CL:0002321!8.29e-07!248
|ontology_enrichment_celltype=CL:0000680!2.14e-17!58;CL:0000056!2.14e-17!58;CL:0000355!2.14e-17!58;CL:0000057!2.31e-17!76;CL:0000187!1.24e-15!55;CL:0000183!1.62e-13!59;CL:0000393!1.41e-12!61;CL:0000211!1.41e-12!61;CL:0000192!5.80e-12!43;CL:0000514!5.80e-12!43;CL:0000055!3.30e-10!106;CL:0000048!3.81e-10!427;CL:0002334!1.11e-09!12;CL:0000359!1.82e-09!32;CL:0000723!2.19e-09!433;CL:0002620!7.37e-09!23;CL:0000034!1.98e-08!441;CL:0000136!8.58e-08!15;CL:0000222!1.08e-07!121;CL:0002494!3.38e-07!16
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!9.01e-19!83;UBERON:0002329!9.01e-19!83;UBERON:0003077!9.01e-19!83;UBERON:0003059!9.01e-19!83;UBERON:0007282!9.01e-19!83;UBERON:0009618!9.01e-19!83;UBERON:0007285!9.01e-19!83;UBERON:0004290!6.68e-18!70;UBERON:0002385!1.97e-17!63;UBERON:0001015!1.97e-17!63;UBERON:0000383!1.97e-17!63;UBERON:0001134!3.63e-17!61;UBERON:0002036!3.63e-17!61;UBERON:0003082!3.63e-17!61;UBERON:0000486!4.50e-17!82;UBERON:0000475!1.33e-15!365;UBERON:0004872!6.38e-15!84;UBERON:0005256!2.82e-13!143;UBERON:0000468!8.65e-13!659;UBERON:0000481!2.32e-12!347;UBERON:0000119!1.22e-11!312;UBERON:0000483!4.29e-11!309;UBERON:0002100!4.32e-11!216;UBERON:0000490!1.61e-10!138;UBERON:0004923!3.27e-10!57;UBERON:0002049!6.78e-10!79;UBERON:0007798!6.78e-10!79;UBERON:0003102!7.75e-10!95;UBERON:0000467!1.65e-09!625;UBERON:0000948!1.79e-09!24;UBERON:0005498!1.79e-09!24;UBERON:0004140!1.79e-09!24;UBERON:0009881!1.79e-09!24;UBERON:0004141!1.79e-09!24;UBERON:0003084!1.79e-09!24;UBERON:0007005!1.79e-09!24;UBERON:0004139!1.79e-09!24;UBERON:0004291!1.79e-09!24;UBERON:0007100!2.41e-09!27;UBERON:0000480!2.91e-09!626;UBERON:0003104!5.10e-09!238;UBERON:0009142!5.10e-09!238;UBERON:0001981!8.57e-09!60;UBERON:0007500!8.57e-09!60;UBERON:0004537!8.57e-09!60;UBERON:0006965!8.57e-09!60;UBERON:0001637!9.39e-09!42;UBERON:0003509!9.39e-09!42;UBERON:0004572!9.39e-09!42;UBERON:0002199!1.15e-08!45;UBERON:0002416!1.15e-08!45;UBERON:0000477!1.43e-08!286;UBERON:0003914!1.84e-08!118;UBERON:0001009!4.79e-08!113;UBERON:0004573!5.34e-08!33;UBERON:0004571!5.34e-08!33;UBERON:0004535!7.55e-08!110;UBERON:0000055!8.59e-08!69;UBERON:0002097!4.73e-07!40;UBERON:0001013!5.75e-07!14
|ontology_enrichment_uberon=UBERON:0002385!9.65e-17!64;UBERON:0001015!9.65e-17!64;UBERON:0000383!9.65e-17!64;UBERON:0001134!3.61e-16!62;UBERON:0002036!3.61e-16!62;UBERON:0003082!3.61e-16!62;UBERON:0007524!6.69e-15!73;UBERON:0002329!8.45e-15!71;UBERON:0003059!8.45e-15!71;UBERON:0007282!8.45e-15!71;UBERON:0004290!8.45e-15!71;UBERON:0009618!8.45e-15!71;UBERON:0003077!2.39e-14!72;UBERON:0007285!2.39e-14!72;UBERON:0000486!1.29e-12!83;UBERON:0007503!6.36e-12!78;UBERON:0004872!1.28e-11!83;UBERON:0000948!9.20e-10!24;UBERON:0005498!9.20e-10!24;UBERON:0004140!9.20e-10!24;UBERON:0009881!9.20e-10!24;UBERON:0004141!9.20e-10!24;UBERON:0003084!9.20e-10!24;UBERON:0007005!9.20e-10!24;UBERON:0004139!9.20e-10!24;UBERON:0004291!9.20e-10!24;UBERON:0000926!1.34e-09!315;UBERON:0004120!1.34e-09!315;UBERON:0006603!1.34e-09!315;UBERON:0003104!2.94e-09!160;UBERON:0009142!2.94e-09!160;UBERON:0005256!5.13e-09!122;UBERON:0007100!1.27e-08!27;UBERON:0004923!2.26e-07!66;UBERON:0003688!6.15e-07!6;UBERON:0002358!6.15e-07!6;UBERON:0003684!6.15e-07!6;UBERON:0001178!6.15e-07!6;UBERON:0002199!6.55e-07!46;UBERON:0002416!6.55e-07!46;UBERON:0004797!6.62e-07!7;UBERON:0001637!6.76e-07!42;UBERON:0003509!6.76e-07!42;UBERON:0004572!6.76e-07!42;UBERON:0004535!7.93e-07!109
|tf_chipseq_enrich=BCLAF1#9774;7:4.33052952202437:0.000958817819544646:0.00689893036551314!EP300#2033;11:2.12895311395586:0.00975513976261023:0.0366824023067347!MAFK#7975;10:7.74306661080855:3.65307166813718e-07:1.80133688360991e-05!NR2C2#7182;8:7.4547682069122:8.71584813982768e-06:0.000235334659740296!POU2F2#5452;9:2.34157475770522:0.0114563203238321:0.0419113996882691!TRIM28#10155;15:7.96736787654108:1.04717244445614e-10:1.13097872726531e-08
|tf_chipseq_enrich=BCLAF1#9774;7:4.33052952202437:0.000958817819544646:0.00689893036551314!EP300#2033;11:2.12895311395586:0.00975513976261023:0.0366824023067347!MAFK#7975;10:7.74306661080855:3.65307166813718e-07:1.80133688360991e-05!NR2C2#7182;8:7.4547682069122:8.71584813982768e-06:0.000235334659740296!POU2F2#5452;9:2.34157475770522:0.0114563203238321:0.0419113996882691!TRIM28#10155;15:7.96736787654108:1.04717244445614e-10:1.13097872726531e-08
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}}
}}

Revision as of 15:00, 19 October 2012


Full id: C333_Fibroblast_Smooth_Preadipocyte_Adipocyte_Ewing_Placental_sacrococcigeal



Phase1 CAGE Peaks

Hg19::chr3:112317985..112318004,-p@chr3:112317985..112318004
-
Hg19::chr3:112318598..112318609,-p@chr3:112318598..112318609
-
Hg19::chr3:112320772..112320784,-p@chr3:112320772..112320784
-
Hg19::chr3:112324034..112324048,-p@chr3:112324034..112324048
-
Hg19::chr3:112356995..112357025,+p@chr3:112356995..112357025
+
Hg19::chr3:112357199..112357228,+p@chr3:112357199..112357228
+
Hg19::chr3:112357559..112357568,-p@chr3:112357559..112357568
-
Hg19::chr3:112357575..112357598,-p@chr3:112357575..112357598
-
Hg19::chr3:112357721..112357731,-p@chr3:112357721..112357731
-
Hg19::chr3:112357721..112357832,+p@chr3:112357721..112357832
+
Hg19::chr3:112357766..112357771,-p@chr3:112357766..112357771
-
Hg19::chr3:112357848..112357858,-p@chr3:112357848..112357858
-
Hg19::chr3:112358008..112358018,-p25@CCDC80
Hg19::chr3:112358055..112358066,-p24@CCDC80
Hg19::chr3:112358125..112358137,-p22@CCDC80
Hg19::chr3:112358228..112358239,-p31@CCDC80
Hg19::chr3:112358263..112358270,-p35@CCDC80
Hg19::chr3:112358632..112358646,-p5@CCDC80
Hg19::chr3:112359190..112359239,-p9@CCDC80
Hg19::chr3:112359295..112359306,-p19@CCDC80
Hg19::chr3:112359358..112359370,-p26@CCDC80
Hg19::chr3:112359375..112359386,-p27@CCDC80
Hg19::chr3:112359471..112359488,-p21@CCDC80
Hg19::chr3:112359502..112359520,-p13@CCDC80
Hg19::chr3:112359529..112359540,-p23@CCDC80
Hg19::chr3:112359550..112359569,-p7@CCDC80
Hg19::chr3:112359574..112359583,-p30@CCDC80
Hg19::chr3:112359611..112359633,-p18@CCDC80
Hg19::chr3:112359634..112359653,-p10@CCDC80
Hg19::chr3:112359654..112359671,-p15@CCDC80
Hg19::chr3:112359698..112359713,-p17@CCDC80
Hg19::chr3:112359729..112359753,+p@chr3:112359729..112359753
+
Hg19::chr3:112359880..112359894,-p2@CCDC80
Hg19::chr3:112359959..112359972,-p3@CCDC80
Hg19::chr3:112359975..112359997,-p1@CCDC80


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
muscle tissue9.65e-1764
musculature9.65e-1764
musculature of body9.65e-1764
skeletal muscle tissue3.61e-1662
striated muscle tissue3.61e-1662
myotome3.61e-1662
dense mesenchyme tissue6.69e-1573
somite8.45e-1571
presomitic mesoderm8.45e-1571
presumptive segmental plate8.45e-1571
dermomyotome8.45e-1571
trunk paraxial mesoderm8.45e-1571
paraxial mesoderm2.39e-1472
presumptive paraxial mesoderm2.39e-1472
multilaminar epithelium1.29e-1283
epithelial vesicle6.36e-1278
splanchnic layer of lateral plate mesoderm1.28e-1183
heart9.20e-1024
primitive heart tube9.20e-1024
primary heart field9.20e-1024
anterior lateral plate mesoderm9.20e-1024
heart tube9.20e-1024
heart primordium9.20e-1024
cardiac mesoderm9.20e-1024
cardiogenic plate9.20e-1024
heart rudiment9.20e-1024
mesoderm1.34e-09315
mesoderm-derived structure1.34e-09315
presumptive mesoderm1.34e-09315
mesenchyme2.94e-09160
entire embryonic mesenchyme2.94e-09160
trunk mesenchyme5.13e-09122
primary circulatory organ1.27e-0827
organ component layer2.26e-0766
omentum6.15e-076
peritoneum6.15e-076
abdominal cavity6.15e-076
visceral peritoneum6.15e-076
integument6.55e-0746
integumental system6.55e-0746
blood vessel layer6.62e-077
artery6.76e-0742
arterial blood vessel6.76e-0742
arterial system6.76e-0742
cardiovascular system7.93e-07109


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
BCLAF1#977474.330529522024370.0009588178195446460.00689893036551314
EP300#2033112.128953113955860.009755139762610230.0366824023067347
MAFK#7975107.743066610808553.65307166813718e-071.80133688360991e-05
NR2C2#718287.45476820691228.71584813982768e-060.000235334659740296
POU2F2#545292.341574757705220.01145632032383210.0419113996882691
TRIM28#10155157.967367876541081.04717244445614e-101.13097872726531e-08



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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