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Coexpression cluster:C3317: Difference between revisions

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|ontology_enrichment_disease=DOID:305!6.16e-23!106;DOID:0050687!2.01e-15!143;DOID:299!2.02e-09!25
|ontology_enrichment_disease=DOID:305!6.16e-23!106;DOID:0050687!2.01e-15!143;DOID:299!2.02e-09!25
|ontology_enrichment_uberon=UBERON:0004119!3.50e-28!169;UBERON:0000925!3.50e-28!169;UBERON:0006595!3.50e-28!169;UBERON:0004921!2.29e-23!129;UBERON:0004185!2.29e-23!129;UBERON:0001007!7.07e-23!155;UBERON:0001555!7.07e-23!155;UBERON:0007026!7.07e-23!155;UBERON:0000077!1.53e-21!130;UBERON:0000466!7.61e-19!126;UBERON:0000464!1.10e-18!104;UBERON:0001041!1.34e-16!98;UBERON:0005177!1.21e-15!107;UBERON:0001004!4.66e-15!72;UBERON:0000062!9.58e-14!511;UBERON:0000481!1.57e-12!347;UBERON:0000065!1.65e-12!53;UBERON:0005911!3.97e-12!82;UBERON:0001048!1.38e-11!168;UBERON:0000922!3.23e-11!612;UBERON:0001008!5.69e-11!45;UBERON:0005153!1.67e-10!37;UBERON:0006554!1.76e-10!44;UBERON:0008947!2.99e-10!38;UBERON:0003258!2.99e-10!38;UBERON:0002553!3.09e-10!70;UBERON:0003104!4.89e-10!238;UBERON:0009142!4.89e-10!238;UBERON:0000063!5.05e-10!97;UBERON:0000468!9.80e-10!659;UBERON:0005178!1.19e-09!34;UBERON:0002224!1.19e-09!34;UBERON:0005181!4.05e-09!35;UBERON:0000064!4.35e-09!219;UBERON:0000072!7.01e-09!46;UBERON:0002050!8.39e-09!605;UBERON:0005423!8.39e-09!605;UBERON:0000058!1.48e-08!26;UBERON:0000923!1.62e-08!604;UBERON:0005291!1.62e-08!604;UBERON:0006598!1.62e-08!604;UBERON:0002532!1.62e-08!604;UBERON:0002048!1.87e-08!22;UBERON:0000117!1.87e-08!22;UBERON:0000171!1.87e-08!22;UBERON:0000170!1.87e-08!22;UBERON:0005597!1.87e-08!22;UBERON:0000118!1.87e-08!22;UBERON:0009569!2.00e-08!113;UBERON:0005409!2.43e-08!35;UBERON:0000160!2.65e-08!27;UBERON:0005156!7.53e-08!59;UBERON:0000990!7.53e-08!59;UBERON:0000161!1.22e-07!35;UBERON:0003886!1.28e-07!63;UBERON:0000489!1.66e-07!32;UBERON:0005157!1.75e-07!51;UBERON:0000467!1.84e-07!625;UBERON:0002113!2.25e-07!27;UBERON:0003918!2.25e-07!27;UBERON:0005095!2.25e-07!27;UBERON:0007687!2.25e-07!27;UBERON:0000480!2.34e-07!626;UBERON:0003133!4.31e-07!48;UBERON:0000475!4.59e-07!365;UBERON:0003135!6.94e-07!11;UBERON:0003064!7.83e-07!37
|ontology_enrichment_uberon=UBERON:0004119!3.50e-28!169;UBERON:0000925!3.50e-28!169;UBERON:0006595!3.50e-28!169;UBERON:0004921!2.29e-23!129;UBERON:0004185!2.29e-23!129;UBERON:0001007!7.07e-23!155;UBERON:0001555!7.07e-23!155;UBERON:0007026!7.07e-23!155;UBERON:0000077!1.53e-21!130;UBERON:0000466!7.61e-19!126;UBERON:0000464!1.10e-18!104;UBERON:0001041!1.34e-16!98;UBERON:0005177!1.21e-15!107;UBERON:0001004!4.66e-15!72;UBERON:0000062!9.58e-14!511;UBERON:0000481!1.57e-12!347;UBERON:0000065!1.65e-12!53;UBERON:0005911!3.97e-12!82;UBERON:0001048!1.38e-11!168;UBERON:0000922!3.23e-11!612;UBERON:0001008!5.69e-11!45;UBERON:0005153!1.67e-10!37;UBERON:0006554!1.76e-10!44;UBERON:0008947!2.99e-10!38;UBERON:0003258!2.99e-10!38;UBERON:0002553!3.09e-10!70;UBERON:0003104!4.89e-10!238;UBERON:0009142!4.89e-10!238;UBERON:0000063!5.05e-10!97;UBERON:0000468!9.80e-10!659;UBERON:0005178!1.19e-09!34;UBERON:0002224!1.19e-09!34;UBERON:0005181!4.05e-09!35;UBERON:0000064!4.35e-09!219;UBERON:0000072!7.01e-09!46;UBERON:0002050!8.39e-09!605;UBERON:0005423!8.39e-09!605;UBERON:0000058!1.48e-08!26;UBERON:0000923!1.62e-08!604;UBERON:0005291!1.62e-08!604;UBERON:0006598!1.62e-08!604;UBERON:0002532!1.62e-08!604;UBERON:0002048!1.87e-08!22;UBERON:0000117!1.87e-08!22;UBERON:0000171!1.87e-08!22;UBERON:0000170!1.87e-08!22;UBERON:0005597!1.87e-08!22;UBERON:0000118!1.87e-08!22;UBERON:0009569!2.00e-08!113;UBERON:0005409!2.43e-08!35;UBERON:0000160!2.65e-08!27;UBERON:0005156!7.53e-08!59;UBERON:0000990!7.53e-08!59;UBERON:0000161!1.22e-07!35;UBERON:0003886!1.28e-07!63;UBERON:0000489!1.66e-07!32;UBERON:0005157!1.75e-07!51;UBERON:0000467!1.84e-07!625;UBERON:0002113!2.25e-07!27;UBERON:0003918!2.25e-07!27;UBERON:0005095!2.25e-07!27;UBERON:0007687!2.25e-07!27;UBERON:0000480!2.34e-07!626;UBERON:0003133!4.31e-07!48;UBERON:0000475!4.59e-07!365;UBERON:0003135!6.94e-07!11;UBERON:0003064!7.83e-07!37
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}}
}}

Revision as of 13:39, 5 September 2012


Full id: C3317_smallcell_lung_merkel_small_kidney_bronchioalveolar_Renal



Phase1 CAGE Peaks

Hg19::chr12:6484605..6484629,-p1@SCNN1A
Hg19::chr12:6484687..6484698,-p6@SCNN1A
Hg19::chr12:6484722..6484736,-p2@SCNN1A


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.50e-28169
endoderm3.50e-28169
presumptive endoderm3.50e-28169
subdivision of digestive tract2.29e-23129
endodermal part of digestive tract2.29e-23129
digestive system7.07e-23155
digestive tract7.07e-23155
primitive gut7.07e-23155
mixed endoderm/mesoderm-derived structure1.53e-21130
immaterial anatomical entity7.61e-19126
anatomical space1.10e-18104
foregut1.34e-1698
trunk region element1.21e-15107
respiratory system4.66e-1572
organ9.58e-14511
multi-tissue structure1.57e-12347
respiratory tract1.65e-1253
endo-epithelium3.97e-1282
primordium1.38e-11168
embryo3.23e-11612
renal system5.69e-1145
epithelial bud1.67e-1037
urinary system structure1.76e-1044
respiratory primordium2.99e-1038
endoderm of foregut2.99e-1038
anatomical cavity3.09e-1070
mesenchyme4.89e-10238
entire embryonic mesenchyme4.89e-10238
organ segment5.05e-1097
multi-cellular organism9.80e-10659
thoracic cavity element1.19e-0934
thoracic cavity1.19e-0934
thoracic segment organ4.05e-0935
organ part4.35e-09219
segment of respiratory tract7.01e-0946
embryonic structure8.39e-09605
developing anatomical structure8.39e-09605
duct1.48e-0826
germ layer1.62e-08604
embryonic tissue1.62e-08604
presumptive structure1.62e-08604
epiblast (generic)1.62e-08604
lung1.87e-0822
respiratory tube1.87e-0822
respiration organ1.87e-0822
pair of lungs1.87e-0822
lung primordium1.87e-0822
lung bud1.87e-0822
subdivision of trunk2.00e-08113
gastrointestinal system2.43e-0835
intestine2.65e-0827
reproductive structure7.53e-0859
reproductive system7.53e-0859
orifice1.22e-0735
body cavity precursor1.28e-0763
cavitated compound organ1.66e-0732
epithelial fold1.75e-0751
anatomical system1.84e-07625
kidney2.25e-0727
kidney mesenchyme2.25e-0727
kidney rudiment2.25e-0727
kidney field2.25e-0727
anatomical group2.34e-07626
reproductive organ4.31e-0748
organism subdivision4.59e-07365
male reproductive organ6.94e-0711
intermediate mesoderm7.83e-0737
Disease
Ontology termp-valuen
carcinoma6.16e-23106
cell type cancer2.01e-15143
adenocarcinoma2.02e-0925


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
CTBP2#1488362.71700033932814.049570681927e-060.000129139881664053
EP300#203336.77394172622320.003216880500103790.0167073341563648
ESR1#2099330.76860329615453.43136389821584e-050.000674638957390369
HDAC2#3066313.41562023662630.0004140761399857210.00390268910603454
JUN#3725312.51282919233630.0005103313992726250.00443415149822244
JUND#372736.994663941871030.002921845042734990.015635321740954
NANOG#79923329.24477848101273.99627955670032e-050.000735319662829854
NR3C1#2908314.9730233311730.0002978331194675480.00308248866951455
POU5F1#54603335.4392014519062.63510205045339e-081.82015491433401e-06
RXRA#6256320.07461713913330.0001235730348432220.00164930916114905
SIN3A#2594235.408884726815140.006318961977991520.0275816470940551
SP1#666735.69838137814090.005403962701712170.0245758528458139
TAF7#6879311.43306940492390.0006690181981945830.00541346491061006
TCF12#6938310.63446490218640.0008313523990202070.00628215130607564
USF1#739136.361499277207960.00388404057290560.0189748953781312



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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