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{{Coexpression_clusters
{{Coexpression_clusters
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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

Revision as of 17:21, 12 September 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 organism1.14e-33115
anatomical conduit8.28e-21241
tube7.10e-20194
anatomical cluster1.08e-19286
cell layer1.34e-13312
epithelium1.77e-13309
endothelium3.23e-1118
blood vessel endothelium3.23e-1118
cardiovascular system endothelium3.23e-1118
epithelial tube3.37e-10118
neural tube4.87e-1057
neural rod4.87e-1057
future spinal cord4.87e-1057
neural keel4.87e-1057
endocrine gland5.80e-1035
neural plate8.20e-1086
presumptive neural plate8.20e-1086
regional part of brain1.57e-0959
brainstem2.69e-098
anatomical system3.68e-09625
anatomical group4.33e-09626
neurectoderm5.80e-0990
simple squamous epithelium1.67e-0822
endocrine system1.91e-0845
central nervous system2.14e-0882
multi-cellular organism2.68e-08659
brain3.38e-0869
future brain3.38e-0869
digestive tract diverticulum4.01e-0823
multi-tissue structure7.36e-08347
subdivision of digestive tract7.87e-08129
endodermal part of digestive tract7.87e-08129
immune organ8.68e-0826
vasculature1.01e-0779
vascular system1.01e-0779
liver1.17e-0719
digestive gland1.17e-0719
liver bud1.17e-0719
vessel1.25e-0769
circulatory system1.38e-07113
endothelial tube2.28e-079
arterial system endothelium2.28e-079
endothelium of artery2.28e-079
lymphoid system2.66e-0710
hepatic diverticulum2.95e-0722
liver primordium2.95e-0722
lymphatic vessel4.06e-078
lymph vasculature4.06e-078
lymphatic part of lymphoid system4.06e-078
squamous epithelium4.62e-0725
large intestine6.76e-0711
sac8.79e-0726


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.

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