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Coexpression cluster:C3608: Difference between revisions

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|full_id=C3608_Renal_ductus_bronchioalveolar_retina_kidney_seminal_Alveolar
|full_id=C3608_Renal_ductus_bronchioalveolar_retina_kidney_seminal_Alveolar
|id=C3608
|id=C3608
|ontology_enrichment_celltype=CL:1000449!1.21e-17!16;CL:1000507!2.40e-16!12;CL:1000494!2.40e-16!12;CL:1000497!2.31e-15!18;CL:0002518!2.31e-15!18;CL:0002681!5.30e-15!13;CL:0002584!5.30e-15!13;CL:0002322!1.70e-11!5;CL:0000239!1.07e-08!3;CL:1000615!1.07e-08!3;CL:0002306!1.07e-08!3
|ontology_enrichment_celltype=CL:1000507!8.40e-30!10;CL:1000494!8.40e-30!10;CL:0002681!8.85e-25!12;CL:0002584!8.85e-25!12;CL:1000449!1.41e-24!15;CL:0002322!7.95e-22!5;CL:1000497!1.72e-21!17;CL:0002518!1.72e-21!17;CL:0000239!4.54e-15!3;CL:1000615!4.54e-15!3;CL:0002306!4.54e-15!3;CL:0000650!4.56e-11!2;CL:1000500!4.56e-11!2;CL:1000618!4.56e-11!2;CL:1001318!4.56e-11!2;CL:0002173!4.56e-11!2;CL:0000075!1.49e-09!27;CL:0000322!2.15e-07!3;CL:1000746!6.81e-07!7;CL:1000612!6.81e-07!7
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000080!8.38e-22!18;UBERON:0002120!8.38e-22!18;UBERON:0004875!8.38e-22!18;UBERON:0005721!8.38e-22!18;UBERON:0005754!8.38e-22!18;UBERON:0007297!8.38e-22!18;UBERON:0000058!1.07e-21!26;UBERON:0006555!1.13e-19!17;UBERON:0005103!1.13e-19!17;UBERON:0000083!1.13e-19!17;UBERON:0009201!1.13e-19!17;UBERON:0004819!1.13e-19!17;UBERON:0006553!1.13e-19!17;UBERON:0003074!1.13e-19!17;UBERON:0003060!1.13e-19!17;UBERON:0004876!2.96e-19!20;UBERON:0002113!2.94e-18!27;UBERON:0003918!2.94e-18!27;UBERON:0005095!2.94e-18!27;UBERON:0007687!2.94e-18!27;UBERON:0003887!3.64e-18!21;UBERON:0004211!1.21e-17!16;UBERON:0001285!1.21e-17!16;UBERON:0007684!1.21e-17!16;UBERON:0003220!1.21e-17!16;UBERON:0004208!1.21e-17!16;UBERON:0009773!2.40e-16!12;UBERON:0001231!2.40e-16!12;UBERON:0004810!2.40e-16!12;UBERON:0001225!5.30e-15!13;UBERON:0008987!5.30e-15!13;UBERON:0000489!9.79e-15!32;UBERON:0001851!8.61e-12!16;UBERON:0005172!1.01e-11!55;UBERON:0005173!1.01e-11!55;UBERON:0006554!5.43e-11!44;UBERON:0000353!5.64e-11!17;UBERON:0001008!1.19e-10!45;UBERON:0000466!1.36e-10!126;UBERON:0000464!1.92e-10!104;UBERON:0003886!2.21e-10!63;UBERON:0003064!2.94e-10!37;UBERON:0002417!4.59e-10!61;UBERON:0000916!4.59e-10!61;UBERON:0002553!6.87e-10!70;UBERON:0005177!2.11e-09!107;UBERON:0006947!9.95e-09!3;UBERON:0004054!9.95e-09!3;UBERON:0006853!1.07e-08!3;UBERON:0007685!1.07e-08!3;UBERON:0004134!1.07e-08!3;UBERON:0009569!1.54e-08!113;UBERON:0003135!3.17e-07!11
|ontology_enrichment_uberon=UBERON:0004810!8.40e-30!10;UBERON:0002113!1.15e-28!26;UBERON:0003918!1.15e-28!26;UBERON:0011143!1.15e-28!26;UBERON:0005095!1.15e-28!26;UBERON:0007687!1.15e-28!26;UBERON:0006555!2.66e-28!16;UBERON:0004819!2.66e-28!16;UBERON:0001225!8.85e-25!12;UBERON:0008987!8.85e-25!12;UBERON:0004211!1.41e-24!15;UBERON:0009773!1.41e-24!15;UBERON:0001231!1.41e-24!15;UBERON:0001285!1.41e-24!15;UBERON:0007684!1.41e-24!15;UBERON:0004208!1.41e-24!15;UBERON:0000489!1.44e-23!31;UBERON:0001851!1.47e-19!15;UBERON:0000353!1.47e-19!15;UBERON:0006554!7.38e-17!47;UBERON:0001008!1.93e-16!48;UBERON:0006947!2.45e-15!3;UBERON:0004054!2.45e-15!3;UBERON:0006853!4.54e-15!3;UBERON:0007685!4.54e-15!3;UBERON:0004134!4.54e-15!3;UBERON:0005172!2.45e-14!54;UBERON:0005173!2.45e-14!54;UBERON:0000080!1.87e-13!9;UBERON:0002120!1.87e-13!9;UBERON:0004875!1.87e-13!9;UBERON:0005721!1.87e-13!9;UBERON:0005754!1.87e-13!9;UBERON:0007297!1.87e-13!9;UBERON:0002417!1.37e-12!60;UBERON:0000916!1.37e-12!60;UBERON:0000058!8.36e-12!19;UBERON:0005904!1.28e-11!4;UBERON:0005177!3.76e-11!101;UBERON:0003567!4.56e-11!2;UBERON:0003838!4.56e-11!2;UBERON:0003586!4.56e-11!2;UBERON:0005169!4.56e-11!2;UBERON:0002321!4.56e-11!2;UBERON:0005215!4.56e-11!2;UBERON:0002303!4.56e-11!2;UBERON:0002319!4.56e-11!2;UBERON:0004876!5.97e-11!11;UBERON:0000007!2.42e-10!2;UBERON:0003887!5.20e-10!12;UBERON:0005103!5.31e-10!8;UBERON:0000083!5.31e-10!8;UBERON:0009201!5.31e-10!8;UBERON:0006553!5.31e-10!8;UBERON:0003074!5.31e-10!8;UBERON:0003060!5.31e-10!8;UBERON:0009569!1.17e-09!112;UBERON:0003103!3.43e-09!68;UBERON:0000475!1.41e-07!264;UBERON:0004821!2.15e-07!3;UBERON:0003215!2.15e-07!3;UBERON:0010368!2.15e-07!3;UBERON:0009911!2.15e-07!3;UBERON:0002299!2.15e-07!3;UBERON:0006524!2.15e-07!3;UBERON:0008874!2.15e-07!3;UBERON:0002169!2.15e-07!3;UBERON:0004894!2.15e-07!3;UBERON:0010532!6.81e-07!7;UBERON:0000074!6.81e-07!7;UBERON:0001229!6.81e-07!7;UBERON:0001230!6.81e-07!7;UBERON:0003220!6.81e-07!7;UBERON:0005749!6.81e-07!7;UBERON:0004199!6.81e-07!7;UBERON:0004209!6.81e-07!7;UBERON:0004198!6.81e-07!7
|tf_chipseq_enrich=JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156529661153219!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470778884922955
|tf_chipseq_enrich=JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156529661153219!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470778884922955
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}}
}}

Revision as of 15:15, 19 October 2012


Full id: C3608_Renal_ductus_bronchioalveolar_retina_kidney_seminal_Alveolar



Phase1 CAGE Peaks

Hg19::chr17:171082..171101,+p@chr17:171082..171101
+
Hg19::chr17:171106..171120,+p@chr17:171106..171120
+
Hg19::chr17:171147..171161,+p@chr17:171147..171161
+


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
nephron tubule epithelium8.40e-3010
kidney1.15e-2826
kidney mesenchyme1.15e-2826
upper urinary tract1.15e-2826
kidney rudiment1.15e-2826
kidney field1.15e-2826
excretory tube2.66e-2816
kidney epithelium2.66e-2816
cortex of kidney8.85e-2512
renal parenchyma8.85e-2512
nephron epithelium1.41e-2415
renal tubule1.41e-2415
nephron tubule1.41e-2415
nephron1.41e-2415
uriniferous tubule1.41e-2415
nephrogenic mesenchyme1.41e-2415
cavitated compound organ1.44e-2331
cortex1.47e-1915
parenchyma1.47e-1915
urinary system structure7.38e-1747
renal system1.93e-1648
male genital duct2.45e-153
internal male genitalia2.45e-153
renal cortex tubule4.54e-153
region of nephron tubule4.54e-153
proximal tubule4.54e-153
abdomen element2.45e-1454
abdominal segment element2.45e-1454
mesonephros1.87e-139
pronephros1.87e-139
nephrogenic cord1.87e-139
pronephric mesoderm1.87e-139
rostral part of nephrogenic cord1.87e-139
presumptive pronephric mesoderm1.87e-139
abdominal segment of trunk1.37e-1260
abdomen1.37e-1260
duct8.36e-1219
duct of male reproductive system1.28e-114
trunk region element3.76e-11101
abdomen connective tissue4.56e-112
abdominal segment connective tissue4.56e-112
trunk connective tissue4.56e-112
interstitial tissue4.56e-112
extraglomerular mesangium4.56e-112
kidney interstitium4.56e-112
juxtaglomerular apparatus4.56e-112
mesangium4.56e-112
urogenital ridge5.97e-1111
pituitary gland2.42e-102
intraembryonic coelom5.20e-1012
mesonephric epithelium5.31e-108
mesonephric tubule5.31e-108
nephric duct5.31e-108
renal duct5.31e-108
mesonephric duct5.31e-108
pronephric duct5.31e-108
subdivision of trunk1.17e-09112
compound organ3.43e-0968
organism subdivision1.41e-07264
pulmonary alveolus epithelium2.15e-073
alveolus2.15e-073
pulmonary lobule2.15e-073
lobule2.15e-073
alveolus of lung2.15e-073
alveolar system2.15e-073
pulmonary acinus2.15e-073
alveolar sac2.15e-073
alveolar wall2.15e-073
primitive nephron6.81e-077
renal glomerulus6.81e-077
renal corpuscle6.81e-077
glomerular capsule6.81e-077
metanephric mesenchyme6.81e-077
glomerular tuft6.81e-077
S-shaped body6.81e-077
renal vesicle6.81e-077
comma-shaped body6.81e-077


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)

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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
JUND#372736.994663941871030.002921845042734990.0156529661153219
NRF1#4899312.21027944771090.0005492172401020010.00470778884922955



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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