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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3384_lung_amniotic_signet_papillotubular_prostate_gall_Hepatocyte
|full_id=C3384_lung_amniotic_signet_papillotubular_prostate_gall_Hepatocyte
|id=C3384
|id=C3384

Revision as of 16:17, 12 September 2012


Full id: C3384_lung_amniotic_signet_papillotubular_prostate_gall_Hepatocyte



Phase1 CAGE Peaks

Hg19::chr13:76334798..76334809,+p20@LMO7
Hg19::chr13:76334824..76334862,+p2@LMO7
Hg19::chr13:76334880..76334887,+p34@LMO7


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>

Cell Type
Ontology termp-valuen
epithelial cell6.55e-15254
endodermal cell6.33e-1259
endo-epithelial cell5.36e-1043
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.72e-26169
endoderm4.72e-26169
presumptive endoderm4.72e-26169
subdivision of digestive tract1.20e-24129
endodermal part of digestive tract1.20e-24129
digestive system2.01e-23155
digestive tract2.01e-23155
primitive gut2.01e-23155
mixed endoderm/mesoderm-derived structure9.84e-22130
adult organism1.94e-20115
foregut1.71e-1898
respiratory system2.28e-1572
endo-epithelium6.09e-1582
respiratory tract7.35e-1553
respiratory primordium2.32e-1238
endoderm of foregut2.32e-1238
segment of respiratory tract4.07e-1146
multi-tissue structure1.24e-10347
trunk region element3.03e-10107
organ part5.60e-10219
epithelial bud1.05e-0937
gut epithelium2.78e-0954
organ4.02e-09511
epithelial fold5.59e-0951
immaterial anatomical entity6.61e-09126
cerebral hemisphere3.92e-0832
regional part of cerebral cortex1.03e-0722
gland1.30e-0759
telencephalon1.54e-0734
upper respiratory tract1.80e-0719
anterior neural tube1.95e-0742
regional part of forebrain2.24e-0741
forebrain2.24e-0741
future forebrain2.24e-0741
mesenchyme3.02e-07238
entire embryonic mesenchyme3.02e-07238
regional part of telencephalon3.06e-0733
thoracic segment organ3.23e-0735
neocortex4.76e-0720
lung6.60e-0722
respiratory tube6.60e-0722
respiration organ6.60e-0722
pair of lungs6.60e-0722
lung primordium6.60e-0722
lung bud6.60e-0722
thoracic cavity element8.31e-0734
thoracic cavity8.31e-0734
larynx8.82e-079
Disease
Ontology termp-valuen
carcinoma7.86e-21106
cell type cancer1.72e-10143


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000284026158402125
CEBPB#105137.971147625824820.001974187055288560.0115044147900503
CTCF#1066435.360256373075030.0064925092527670.0278777771594677
EP300#203336.77394172622320.003216880500103790.0167131520520515
FOXA1#3169311.08141974938550.000734755275698670.00580155033179809
FOXA2#3170324.63046375266526.68983856509345e-050.00107110233006254
GTF2F1#2962312.73966087675770.0004835525047438590.00433119554399176
HDAC2#3066313.41562023662630.0004140761399857210.0039037459815823
HNF4A#3172323.13229036295378.07584663437677e-050.001226277037871
HNF4G#3174328.75342252644684.20470658818262e-050.000755566674747427
MAFF#23764356.31535648994525.59409009993116e-060.000168855831198471
MAFK#7975327.10073313782995.02195559325033e-050.000856586673531719
NR3C1#2908314.9730233311730.0002978331194675480.00308279416888714
RAD21#5885310.35503389545630.0009004912073565420.00662671936338147
RFX5#5993312.04791082719510.0005717246050312580.00483562892977483
RXRA#6256320.07461713913330.0001235730348432220.00165015268968052
SIN3A#2594235.408884726815140.006318961977991520.0275885652781847
SMC3#9126315.04493284493280.0002935825420371870.00308465463861386
SP1#666735.69838137814090.005403962701712170.0245854879161926
STAT3#6774310.51946499715420.0008589184530415310.00641847340563856
TCF7L2#6934310.77017656313730.0008003181298398380.00612429844389968



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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