Personal tools

Coexpression cluster:C1011

From FANTOM5_SSTAR

Revision as of 05:16, 21 June 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1011_acute_granulocyte_Hodgkin_neuroepithelioma_retinoblastoma_hepatoblastoma_merkel



Phase1 CAGE Peaks

  Short description
Hg19::chr12:133263893..133263986,- p1@POLE
Hg19::chr19:10305581..10305646,- p1@DNMT1
Hg19::chr19:4402613..4402658,+ p1@CHAF1A
Hg19::chr19:48673580..48673630,- p1@LIG1
Hg19::chr19:50887585..50887619,+ p1@POLD1
Hg19::chr8:145669791..145669834,- p1@TONSL
Hg19::chr8:145743164..145743236,- p1@RECQL4
Hg19::chr8:145743237..145743261,- p2@RECQL4


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0006281DNA repair1.36711281599438e-07
GO:0006974response to DNA damage stimulus1.36711281599438e-07
GO:0006259DNA metabolic process1.36711281599438e-07
GO:0009719response to endogenous stimulus2.2353665367932e-07
GO:0006260DNA replication5.81249790921492e-06
GO:0006950response to stress9.73788887599282e-06
GO:0000731DNA synthesis during DNA repair1.30963982036091e-05
GO:0003682chromatin binding1.70270067455608e-05
GO:0007049cell cycle9.94130900183607e-05
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00043621865655787
GO:0003887DNA-directed DNA polymerase activity0.000449255144653721
GO:0005634nucleus0.000449255144653721
GO:0051329interphase of mitotic cell cycle0.00119150193290442
GO:0051325interphase0.00124071983685884
GO:0043283biopolymer metabolic process0.00182299496202717
GO:0043231intracellular membrane-bound organelle0.00296693105816845
GO:0043227membrane-bound organelle0.00296693105816845
GO:0006335DNA replication-dependent nucleosome assembly0.00296693105816845
GO:0045875negative regulation of sister chromatid cohesion0.00296693105816845
GO:0007063regulation of sister chromatid cohesion0.00296693105816845
GO:0006310DNA recombination0.0039538293047545
GO:0016779nucleotidyltransferase activity0.00494415731932331
GO:0003891delta DNA polymerase activity0.00494415731932331
GO:0003910DNA ligase (ATP) activity0.00494415731932331
GO:0003886DNA (cytosine-5-)-methyltransferase activity0.00549310385928867
GO:0003893epsilon DNA polymerase activity0.00549310385928867
GO:0003909DNA ligase activity0.00549310385928867
GO:0043229intracellular organelle0.00574075701982397
GO:0043226organelle0.00574075701982397
GO:0009008DNA-methyltransferase activity0.00574075701982397
GO:0005678chromatin assembly complex0.00574075701982397
GO:0003676nucleic acid binding0.00618596197214122
GO:0043170macromolecule metabolic process0.00633756424988399
GO:0000278mitotic cell cycle0.00663322789314192
GO:0003677DNA binding0.00686763962456978
GO:0007062sister chromatid cohesion0.00741350756267838
GO:0022403cell cycle phase0.00778579769906605
GO:0016886ligase activity, forming phosphoric ester bonds0.0109211497937796
GO:0048705skeletal morphogenesis0.0112381757070516
GO:0044237cellular metabolic process0.0112381757070516
GO:0008270zinc ion binding0.0112381757070516
GO:0044238primary metabolic process0.0112443768708326
GO:0000084S phase of mitotic cell cycle0.0114891233863831
GO:0000166nucleotide binding0.0114891233863831
GO:0044424intracellular part0.0114891233863831
GO:0000792heterochromatin0.0127739844957742
GO:0051276chromosome organization and biogenesis0.0127739844957742
GO:0051320S phase0.0129621865307859
GO:0006305DNA alkylation0.0136268075946318
GO:0006306DNA methylation0.0136268075946318
GO:0022402cell cycle process0.0158980673489082
GO:0006304DNA modification0.0159452447403155
GO:0046914transition metal ion binding0.0161135256749198
GO:0005657replication fork0.0175430415041266
GO:0009411response to UV0.0177610225540556
GO:0000082G1/S transition of mitotic cell cycle0.0179711408745799
GO:0016458gene silencing0.0197272102767894
GO:0005622intracellular0.0205585703501337
GO:0016585chromatin remodeling complex0.0205585703501337
GO:0043414biopolymer methylation0.0221816836641472
GO:0003678DNA helicase activity0.023750440581921
GO:0007059chromosome segregation0.0281155259347484
GO:0040029regulation of gene expression, epigenetic0.0304696161599306
GO:0032259methylation0.0326956260140766
GO:0004527exonuclease activity0.0326956260140766
GO:0009653anatomical structure morphogenesis0.0333618840509839
GO:0016740transferase activity0.0350776076463905
GO:0009416response to light stimulus0.0350776076463905
GO:0043169cation binding0.0350776076463905
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0362262712413766
GO:0046872metal ion binding0.0411364456418694
GO:0009314response to radiation0.0413173911846125
GO:0043167ion binding0.0425175439882766



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data

disease_data


Cell Type
Ontology termp-valuen
epithelial cell1.98e-14254
Disease
Ontology termp-valuen
cancer9.52e-46235
disease of cellular proliferation1.57e-43239
hematologic cancer2.12e-2651
immune system cancer2.12e-2651
organ system cancer8.38e-24137
leukemia3.24e-2339
cell type cancer1.07e-21143
myeloid leukemia2.47e-1931
carcinoma1.21e-17106


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.