Personal tools

Coexpression cluster:C411

From FANTOM5_SSTAR

Revision as of 10:45, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C411_vagina_Mast_breast_heart_CD14_aorta_liver



Phase1 CAGE Peaks

  Short description
Hg19::chr11:133904003..133904027,- p@chr11:133904003..133904027
-
Hg19::chr11:133907166..133907180,+ p2@ENST00000531938
Hg19::chr11:133907234..133907249,+ p3@ENST00000531938
Hg19::chr11:133907376..133907387,+ p5@ENST00000531938
Hg19::chr11:65374430..65374474,- p5@MAP3K11
Hg19::chr12:2903742..2903763,- p3@CBX3P4
Hg19::chr12:2903775..2903794,- p2@CBX3P4
Hg19::chr12:57082286..57082368,+ p@chr12:57082286..57082368
+
Hg19::chr13:31736027..31736053,- p1@HSPH1
Hg19::chr14:70195360..70195363,- p@chr14:70195360..70195363
-
Hg19::chr14:77924458..77924475,+ p2@AHSA1
Hg19::chr16:87378830..87378846,- p@chr16:87378830..87378846
-
Hg19::chr16:89930250..89930272,- p1@AK098674
Hg19::chr16:89930279..89930301,- p2@AK098674
Hg19::chr18:19284854..19284899,+ p2@MIB1
Hg19::chr19:14629195..14629216,- p1@DNAJB1
Hg19::chr1:245026181..245026208,- p19@HNRNPU
Hg19::chr22:43041411..43041417,+ p@chr22:43041411..43041417
+
Hg19::chr4:88343933..88343946,+ p6@NUDT9
Hg19::chr6:31783311..31783328,+ p1@HSPA1A
p1@HSPA1B
Hg19::chr6:31789738..31789757,- p@chr6:31789738..31789757
-
Hg19::chr6:31795506..31795525,+ p2@HSPA1A
p2@HSPA1B
Hg19::chr7:75923952..75923971,- p@chr7:75923952..75923971
-
Hg19::chr7:75924283..75924306,+ p@chr7:75924283..75924306
+
Hg19::chr7:75931755..75931775,- p@chr7:75931755..75931775
-


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


p.valueFDRnGenesnPathwayName
2.54761513593594e-050.0161264038104745232{HSPA8,34} (Static Module):NA



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:0051789response to protein stimulus5.16481965377491e-05
GO:0006986response to unfolded protein5.16481965377491e-05
GO:0009607response to biotic stimulus0.00408991908245404
GO:0006950response to stress0.0113033427993079
GO:0030189chaperone activator activity0.0131932179441893
GO:0042221response to chemical stimulus0.0167213722932249
GO:0019144ADP-sugar diphosphatase activity0.0183373558696005
GO:0005737cytoplasm0.0183373558696005
GO:0047631ADP-ribose diphosphatase activity0.0197851668314843
GO:0004706JUN kinase kinase kinase activity0.0197851668314843
GO:0051082unfolded protein binding0.0273491196999661
GO:0001671ATPase activator activity0.0274729278152382
GO:0005739mitochondrion0.0320692916310955
GO:0001947heart looping0.0320692916310955
GO:0044424intracellular part0.0320692916310955
GO:0045665negative regulation of neuron differentiation0.0320692916310955
GO:0051085chaperone cofactor-dependent protein folding0.0320692916310955
GO:0016071mRNA metabolic process0.0320692916310955
GO:0044444cytoplasmic part0.0320692916310955
GO:0006457protein folding0.0320692916310955
GO:0005524ATP binding0.0320692916310955
GO:0032559adenyl ribonucleotide binding0.0320692916310955
GO:0003007heart morphogenesis0.0320692916310955
GO:0051084'de novo' posttranslational protein folding0.0320692916310955
GO:0001839neural plate morphogenesis0.0320692916310955
GO:0051087chaperone binding0.0320692916310955
GO:0001841neural tube formation0.0320692916310955
GO:0006458'de novo' protein folding0.0320692916310955
GO:0001840neural plate development0.0320692916310955
GO:0000080G1 phase of mitotic cell cycle0.0320692916310955
GO:0001838embryonic epithelial tube formation0.0320692916310955
GO:0045807positive regulation of endocytosis0.0320692916310955
GO:0030530heterogeneous nuclear ribonucleoprotein complex0.0320692916310955
GO:0004709MAP kinase kinase kinase activity0.0320692916310955
GO:0001756somitogenesis0.0320692916310955
GO:0030554adenyl nucleotide binding0.0320692916310955
GO:0046328regulation of JNK cascade0.0320692916310955
GO:0051318G1 phase0.0320692916310955
GO:0021915neural tube development0.0320692916310955
GO:0007257activation of JNK activity0.0343930784770196
GO:0016331morphogenesis of embryonic epithelium0.0343930784770196
GO:0043229intracellular organelle0.0343930784770196
GO:0043226organelle0.0343930784770196
GO:0043507positive regulation of JNK activity0.0343930784770196
GO:0043506regulation of JNK activity0.0365444265241635
GO:0045664regulation of neuron differentiation0.0371756059842438
GO:0035282segmentation0.037779597917854
GO:0006402mRNA catabolic process0.0397233584196399
GO:0005227calcium activated cation channel activity0.0446830244551175
GO:0030100regulation of endocytosis0.0446830244551175
GO:0032553ribonucleotide binding0.0447701239990005
GO:0032555purine ribonucleotide binding0.0447701239990005
GO:0051050positive regulation of transport0.047090896044346
GO:0017076purine nucleotide binding0.0491008753794253



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


uberon_data


Uber Anatomy
Ontology termp-valuen
adult organism7.91e-29115
neural tube1.59e-1857
neural rod1.59e-1857
future spinal cord1.59e-1857
neural keel1.59e-1857
organ1.77e-18511
anterior neural tube6.40e-1442
regional part of forebrain2.60e-1341
forebrain2.60e-1341
future forebrain2.60e-1341
regional part of brain3.22e-1359
neural plate6.06e-1286
presumptive neural plate6.06e-1286
neurectoderm7.67e-1290
brain1.64e-1169
future brain1.64e-1169
central nervous system3.50e-1182
gray matter1.59e-1034
brain grey matter1.59e-1034
telencephalon3.23e-1034
multi-cellular organism3.91e-10659
regional part of telencephalon5.61e-1033
anatomical system9.49e-10625
regional part of nervous system1.08e-0994
nervous system1.08e-0994
embryo1.49e-09612
anatomical group1.87e-09626
cerebral hemisphere3.44e-0932
anatomical conduit3.63e-09241
embryonic structure7.25e-09605
developing anatomical structure7.25e-09605
tube1.18e-08194
germ layer1.26e-08604
embryonic tissue1.26e-08604
presumptive structure1.26e-08604
epiblast (generic)1.26e-08604
anatomical cluster1.72e-08286
anterior region of body1.72e-08129
craniocervical region1.72e-08129
organ part4.21e-08219
head1.07e-07123
pre-chordal neural plate2.28e-0761
regional part of cerebral cortex2.60e-0722
ectoderm7.37e-07173
presumptive ectoderm7.37e-07173
ectoderm-derived structure8.76e-07169


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.