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Difference between revisions of "Coexpression cluster:C4290"

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|full_id=C4290_Lymphatic_Hepatocyte_liver_adipose_breast_Renal_vagina
 
|full_id=C4290_Lymphatic_Hepatocyte_liver_adipose_breast_Renal_vagina
 
|id=C4290
 
|id=C4290
|ontology_enrichment_celltype=CL:0002139!1.13e-18!24;CL:0000115!2.74e-15!35;CL:0002078!7.74e-12!44;CL:0000071!3.23e-11!18;CL:0002546!3.23e-11!18;CL:0005020!6.44e-10!6;CL:0002138!6.44e-10!6;CL:0005022!6.44e-10!6;CL:0000213!2.53e-08!57;CL:0000215!2.53e-08!57;CL:1000413!2.28e-07!9;CL:0000181!5.16e-07!12;CL:0000417!5.16e-07!12;CL:0000668!5.16e-07!12;CL:0000414!5.16e-07!12;CL:0000412!5.16e-07!12;CL:0000182!5.16e-07!12
+
|ontology_enrichment_celltype=CL:0002139!1.56e-23!24;CL:0000115!2.48e-18!36;CL:0005020!1.52e-15!6;CL:0002138!1.52e-15!6;CL:0005022!1.52e-15!6;CL:0002078!2.34e-15!45;CL:0000071!4.01e-12!18;CL:0002546!4.01e-12!18;CL:0000213!9.15e-11!58;CL:0000215!9.15e-11!58;CL:1000413!1.11e-09!9;CL:0000181!4.40e-09!12;CL:0000417!4.40e-09!12;CL:0000668!4.40e-09!12;CL:0000412!4.40e-09!12;CL:0000182!4.40e-09!12;CL:0002544!8.40e-07!6
 
|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.14e-33!115;UBERON:0004111!8.28e-21!241;UBERON:0000025!7.10e-20!194;UBERON:0000477!1.08e-19!286;UBERON:0000119!1.34e-13!312;UBERON:0000483!1.77e-13!309;UBERON:0001986!3.23e-11!18;UBERON:0004638!3.23e-11!18;UBERON:0004852!3.23e-11!18;UBERON:0003914!3.37e-10!118;UBERON:0001049!4.87e-10!57;UBERON:0005068!4.87e-10!57;UBERON:0006241!4.87e-10!57;UBERON:0007135!4.87e-10!57;UBERON:0002368!5.80e-10!35;UBERON:0003075!8.20e-10!86;UBERON:0007284!8.20e-10!86;UBERON:0002616!1.57e-09!59;UBERON:0002298!2.69e-09!8;UBERON:0000467!3.68e-09!625;UBERON:0000480!4.33e-09!626;UBERON:0002346!5.80e-09!90;UBERON:0000487!1.67e-08!22;UBERON:0000949!1.91e-08!45;UBERON:0001017!2.14e-08!82;UBERON:0000468!2.68e-08!659;UBERON:0005743!2.95e-08!86;UBERON:0000955!3.38e-08!69;UBERON:0006238!3.38e-08!69;UBERON:0009854!4.01e-08!23;UBERON:0000481!7.36e-08!347;UBERON:0004921!7.87e-08!129;UBERON:0004185!7.87e-08!129;UBERON:0005057!8.68e-08!26;UBERON:0002049!1.01e-07!79;UBERON:0007798!1.01e-07!79;UBERON:0002107!1.17e-07!19;UBERON:0006925!1.17e-07!19;UBERON:0008836!1.17e-07!19;UBERON:0000055!1.25e-07!69;UBERON:0001009!1.38e-07!113;UBERON:0003915!2.28e-07!9;UBERON:0004700!2.28e-07!9;UBERON:0001917!2.28e-07!9;UBERON:0002465!2.66e-07!10;UBERON:0008835!2.95e-07!22;UBERON:0003894!2.95e-07!22;UBERON:0001473!4.06e-07!8;UBERON:0004536!4.06e-07!8;UBERON:0006558!4.06e-07!8;UBERON:0006914!4.62e-07!25;UBERON:0000059!6.76e-07!11;UBERON:0009856!8.79e-07!26
+
|ontology_enrichment_uberon=UBERON:0007023!9.91e-19!114;UBERON:0004111!4.02e-16!240;UBERON:0000025!4.51e-13!192;UBERON:0000477!1.04e-12!373;UBERON:0004638!4.01e-12!18;UBERON:0001986!4.01e-12!18;UBERON:0004852!4.01e-12!18;UBERON:0001473!1.97e-11!8;UBERON:0004536!1.97e-11!8;UBERON:0006558!1.97e-11!8;UBERON:0002107!2.68e-11!19;UBERON:0006925!2.68e-11!19;UBERON:0008836!2.68e-11!19;UBERON:0002368!2.06e-10!35;UBERON:0003915!1.11e-09!9;UBERON:0004700!1.11e-09!9;UBERON:0001917!1.11e-09!9;UBERON:0000487!1.65e-09!22;UBERON:0008835!1.88e-09!22;UBERON:0003894!1.88e-09!22;UBERON:0003914!5.36e-09!117;UBERON:0002465!5.76e-09!10;UBERON:0009854!6.03e-09!23;UBERON:0000949!1.52e-08!45;UBERON:0006914!4.18e-08!25;UBERON:0007499!4.67e-08!25;UBERON:0009497!4.67e-08!25;UBERON:0000015!4.67e-08!25;UBERON:0002423!4.67e-08!25;UBERON:0006235!4.67e-08!25;UBERON:0004161!4.67e-08!25;UBERON:0009856!1.15e-07!26;UBERON:0000483!1.23e-07!306;UBERON:0005172!1.64e-07!54;UBERON:0005173!1.64e-07!54;UBERON:0000055!1.77e-07!68;UBERON:0000119!1.89e-07!309;UBERON:0005177!2.45e-07!101;UBERON:0002049!8.12e-07!78;UBERON:0007798!8.12e-07!78
 
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280426457340667!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463752368934546!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167933511221803!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00899883555226144!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582710200005265!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.0010747270418394!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00437915474828699!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392464815173507!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123128955714989!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000758830743672377!JUN#3725;3:12.5128291923363:0.000510331399272625:0.0044530454514691!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.0030953719936383!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165608163556927!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247265919213195!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00615859307120121
 
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280426457340667!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463752368934546!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167933511221803!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00899883555226144!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582710200005265!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.0010747270418394!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00437915474828699!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392464815173507!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123128955714989!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000758830743672377!JUN#3725;3:12.5128291923363:0.000510331399272625:0.0044530454514691!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.0030953719936383!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165608163556927!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247265919213195!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00615859307120121
 
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}}
 
}}

Revision as of 06:49, 19 October 2012


Full id: C4290_Lymphatic_Hepatocyte_liver_adipose_breast_Renal_vagina



Phase1 CAGE Peaks

Hg19::chr3:145940083..145940098,-p6@PLSCR4
Hg19::chr3:145940126..145940135,-p15@PLSCR4
Hg19::chr3:145940214..145940228,-p14@PLSCR4


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
adult organism9.91e-19114
anatomical conduit4.02e-16240
tube4.51e-13192
anatomical cluster1.04e-12373
blood vessel endothelium4.01e-1218
endothelium4.01e-1218
cardiovascular system endothelium4.01e-1218
lymphatic vessel1.97e-118
lymph vasculature1.97e-118
lymphatic part of lymphoid system1.97e-118
liver2.68e-1119
digestive gland2.68e-1119
liver bud2.68e-1119
endocrine gland2.06e-1035
endothelial tube1.11e-099
arterial system endothelium1.11e-099
endothelium of artery1.11e-099
simple squamous epithelium1.65e-0922
hepatic diverticulum1.88e-0922
liver primordium1.88e-0922
epithelial tube5.36e-09117
lymphoid system5.76e-0910
digestive tract diverticulum6.03e-0923
endocrine system1.52e-0845
squamous epithelium4.18e-0825
epithelial sac4.67e-0825
epithelium of foregut-midgut junction4.67e-0825
anatomical boundary4.67e-0825
hepatobiliary system4.67e-0825
foregut-midgut junction4.67e-0825
septum transversum4.67e-0825
sac1.15e-0726
epithelium1.23e-07306
abdomen element1.64e-0754
abdominal segment element1.64e-0754
vessel1.77e-0768
cell layer1.89e-07309
trunk region element2.45e-07101
vasculature8.12e-0778
vascular system8.12e-0778


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#1066435.360256373075030.0064925092527670.0280426457340667
ELF1#199734.258097958807540.01295179875054610.0463752368934546
EP300#203336.77394172622320.003216880500103790.0167933511221803
FOS#235338.99795530889440.001372499272417130.00899883555226144
FOXA1#3169311.08141974938550.000734755275698670.00582710200005265
FOXA2#3170324.63046375266526.68983856509345e-050.0010747270418394
GATA2#2624312.7449317335540.0004829527704283790.00437915474828699
HDAC2#3066313.41562023662630.0004140761399857210.00392464815173507
HNF4A#3172323.13229036295378.07584663437677e-050.00123128955714989
HNF4G#3174328.75342252644684.20470658818262e-050.000758830743672377
JUN#3725312.51282919233630.0005103313992726250.0044530454514691
NR3C1#2908314.9730233311730.0002978331194675480.0030953719936383
RXRA#6256320.07461713913330.0001235730348432220.00165608163556927
SP1#666735.69838137814090.005403962701712170.0247265919213195
TCF7L2#6934310.77017656313730.0008003181298398380.00615859307120121



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.