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Coexpression cluster:C1162

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Full id: C1162_embryonic_iPS_Keratinocyte_giant_teratocarcinoma_acute_chronic



Phase1 CAGE Peaks

Hg19::chr12:112847354..112847457,-p1@RPL6
Hg19::chr1:24018269..24018274,+p2@RPL11
Hg19::chr1:93297622..93297635,+p2@RPL5
Hg19::chr2:55459786..55459807,+p2@RPS27A
Hg19::chr3:185136568..185136602,-p1@ENST00000422486
Hg19::chrX:71497077..71497133,-p1@RPS4X
Hg19::chrX:71497148..71497163,-p3@RPS4X


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


p.valueFDRnGenesnPathwayName
3.11437028550525e-131.04170377464436e-10592Ribosome (KEGG):03010
3.29132314263622e-131.04170377464436e-10593Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.1591439383194e-101.22289685492696e-085296Metabolism of proteins (Reactome):REACT_17015
9.29699977867239e-131.96166695329987e-105114Regulation of beta-cell development (Reactome):REACT_13698
6.81527814787627e-105.3925888345071e-085421Gene Expression (Reactome):REACT_71
1.5108164748526e-101.36620975511671e-085312Diabetes pathways (Reactome):REACT_15380
2.94043896828612e-123.72259573385023e-105143Influenza Infection (Reactome):REACT_6167
2.45472569124687e-123.72259573385023e-105138{RPS27A,138} (Static Module):NA



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


GO IDGO nameFDR corrected p-value
GO:0005830cytosolic ribosome (sensu Eukaryota)1.80412952534817e-08
GO:0044445cytosolic part3.89335864396034e-07
GO:0033279ribosomal subunit4.50106557389469e-07
GO:0019843rRNA binding4.50106557389469e-07
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)4.6083793122753e-07
GO:0015934large ribosomal subunit7.85433413948777e-06
GO:0005829cytosol8.99367102257202e-06
GO:0003735structural constituent of ribosome2.76395189313524e-05
GO:0005840ribosome3.48041401227949e-05
GO:0003723RNA binding5.48133301770672e-05
GO:0030529ribonucleoprotein complex9.14479151801551e-05
GO:0006412translation0.000105937742458961
GO:0009059macromolecule biosynthetic process0.000273606126740663
GO:0044249cellular biosynthetic process0.000593938698888462
GO:0010467gene expression0.00117137004948452
GO:0044267cellular protein metabolic process0.00117327045102701
GO:0044260cellular macromolecule metabolic process0.00117327045102701
GO:0009058biosynthetic process0.00117327045102701
GO:0019538protein metabolic process0.00132208046366353
GO:0043232intracellular non-membrane-bound organelle0.00199327017675962
GO:0043228non-membrane-bound organelle0.00199327017675962
GO:0008582regulation of synaptic growth at neuromuscular junction0.00202360627664
GO:0051124synaptic growth at neuromuscular junction0.00202360627664
GO:0042062long-term strengthening of neuromuscular junction0.00202360627664
GO:00080975S rRNA binding0.00291382148067808
GO:0005737cytoplasm0.00328504115132846
GO:0032991macromolecular complex0.0047323211441893
GO:0050806positive regulation of synaptic transmission0.00520233369326765
GO:0044446intracellular organelle part0.00541624347566376
GO:0044422organelle part0.00541624347566376
GO:0051971positive regulation of transmission of nerve impulse0.0054817063055444
GO:0031646positive regulation of neurological process0.00606867467450403
GO:0007528neuromuscular junction development0.00721681283175408
GO:0044444cytoplasmic part0.00721681283175408
GO:0030433ER-associated protein catabolic process0.00741595907656725
GO:0006515misfolded or incompletely synthesized protein catabolic process0.00741595907656725
GO:0048167regulation of synaptic plasticity0.0102161128062905
GO:0050804regulation of synaptic transmission0.0102161128062905
GO:0051969regulation of transmission of nerve impulse0.0109171849772188
GO:0050803regulation of synapse structure and activity0.0109171849772188
GO:0043229intracellular organelle0.0125611320158036
GO:0043226organelle0.0125611320158036
GO:0043161proteasomal ubiquitin-dependent protein catabolic process0.0129726795143152
GO:0031644regulation of neurological process0.0134724526218766
GO:0007416synaptogenesis0.0134724526218766
GO:0043170macromolecule metabolic process0.0136164574474217
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.0175335600722431
GO:0003676nucleic acid binding0.0181231096858235
GO:0048589developmental growth0.0182986050132503
GO:0050808synapse organization and biogenesis0.0188997388298272
GO:0048741skeletal muscle fiber development0.0195672790731445
GO:0048747muscle fiber development0.0195672790731445
GO:0044237cellular metabolic process0.0224350864349877
GO:0044238primary metabolic process0.0228668393165134
GO:0044424intracellular part0.0242061947206519
GO:0007411axon guidance0.0242061947206519
GO:0007519skeletal muscle development0.0284344745885562
GO:0016567protein ubiquitination0.0304359394801792
GO:0032446protein modification by small protein conjugation0.0315521008867531
GO:0043062extracellular structure organization and biogenesis0.0338328528209046
GO:0014706striated muscle development0.0348546835516022
GO:0005622intracellular0.0432642044174568
GO:0007409axonogenesis0.0436523682379881
GO:0048667neuron morphogenesis during differentiation0.0442085182750772
GO:0048812neurite morphogenesis0.0442085182750772
GO:0015935small ribosomal subunit0.0442085182750772
GO:0000904cellular morphogenesis during differentiation0.0453348748357801
GO:0031175neurite development0.0478334177117967



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
somite1.84e-1183
paraxial mesoderm1.84e-1183
presomitic mesoderm1.84e-1183
presumptive segmental plate1.84e-1183
trunk paraxial mesoderm1.84e-1183
presumptive paraxial mesoderm1.84e-1183
dermomyotome4.43e-1170
multilaminar epithelium1.84e-1082
unilaminar epithelium1.99e-10138
mesenchyme2.58e-10238
entire embryonic mesenchyme2.58e-10238
skeletal muscle tissue9.66e-0961
striated muscle tissue9.66e-0961
myotome9.66e-0961
artery7.51e-0842
arterial blood vessel7.51e-0842
arterial system7.51e-0842
muscle tissue1.01e-0763
musculature1.01e-0763
musculature of body1.01e-0763
trunk1.16e-07216
trunk mesenchyme5.10e-07143
larynx6.41e-079
Disease
Ontology termp-valuen
disease of cellular proliferation4.75e-31239
cancer1.06e-29235
cell type cancer6.85e-15143
carcinoma3.39e-14106
organ system cancer2.04e-13137
hematologic cancer1.93e-0851
immune system cancer1.93e-0851


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


No analysis results for this cluster

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.