Personal tools

Coexpression cluster:C361

From FANTOM5_SSTAR

Revision as of 14:38, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C361_Neural_Astrocyte_Neurons_spinal_Chondrocyte_Fibroblast_sacrococcigeal



Phase1 CAGE Peaks

Hg19::chr11:33912780..33912786,-p@chr11:33912780..33912786
-
Hg19::chr12:106976837..106976850,+p5@RFX4
Hg19::chr12:56075553..56075558,+p5@METTL7B
Hg19::chr14:29236460..29236467,+p12@FOXG1
Hg19::chr14:51562037..51562053,-p2@TRIM9
Hg19::chr17:61228693..61228707,+p@chr17:61228693..61228707
+
Hg19::chr19:19356203..19356221,+p@chr19:19356203..19356221
+
Hg19::chr1:205306210..205306228,-p@chr1:205306210..205306228
-
Hg19::chr1:205325850..205325870,-p2@KLHDC8A
Hg19::chr1:23696308..23696339,-p2@ZNF436
Hg19::chr1:23696348..23696363,-p4@ZNF436
Hg19::chr20:20472232..20472244,-p@chr20:20472232..20472244
-
Hg19::chr21:34186006..34186019,-p2@C21orf62
Hg19::chr2:210288885..210288888,+p33@MAP2
Hg19::chr3:62228762..62228795,+p6@PTPRG
Hg19::chr3:62228807..62228819,+p10@PTPRG
Hg19::chr3:78719376..78719409,-p8@ROBO1
Hg19::chr3:78719410..78719451,-p5@ROBO1
Hg19::chr3:78719667..78719679,-p17@ROBO1
Hg19::chr4:48545900..48545919,-p@chr4:48545900..48545919
-
Hg19::chr4:48545952..48545965,-p@chr4:48545952..48545965
-
Hg19::chr5:140857085..140857104,+p@chr5:140857085..140857104
+
Hg19::chr5:63510296..63510308,+p@chr5:63510296..63510308
+
Hg19::chr7:121513374..121513415,+p5@PTPRZ1
Hg19::chr7:121513478..121513517,+p4@PTPRZ1
Hg19::chr7:121513532..121513545,+p6@PTPRZ1
Hg19::chr7:137028222..137028235,-p7@PTN
Hg19::chr7:137028246..137028346,-p1@PTN
Hg19::chr7:137028364..137028380,-p4@PTN
Hg19::chr7:137028392..137028410,-p5@PTN
Hg19::chr9:126774091..126774098,+p4@LHX2


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

GO IDGO nameFDR corrected p-value
GO:0007399nervous system development0.000557336611267514
GO:0019198transmembrane receptor protein phosphatase activity0.00126058469449034
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.00126058469449034
GO:0007417central nervous system development0.00332990684368422
GO:0004089carbonate dehydratase activity0.00416377714289835
GO:0048731system development0.00453165753797798
GO:0048856anatomical structure development0.0109183876950834
GO:0016836hydro-lyase activity0.0109183876950834
GO:0016835carbon-oxygen lyase activity0.012211174528187
GO:0007275multicellular organismal development0.0145106528423907
GO:0008046axon guidance receptor activity0.0172644645043749
GO:0007420brain development0.0172644645043749
GO:0006730one-carbon compound metabolic process0.0197690695565447
GO:0007185transmembrane receptor protein tyrosine phosphatase signaling pathway0.0273903705317438
GO:0050789regulation of biological process0.0273903705317438
GO:0004725protein tyrosine phosphatase activity0.0314416979328173
GO:0006470protein amino acid dephosphorylation0.037793969519023
GO:0065007biological regulation0.0387732940610384
GO:0032502developmental process0.0387732940610384
GO:0016829lyase activity0.0387732940610384
GO:0016311dephosphorylation0.0387732940610384
GO:0050772positive regulation of axonogenesis0.0387732940610384
GO:0007610behavior0.0387732940610384
GO:0007167enzyme linked receptor protein signaling pathway0.0387732940610384
GO:0009888tissue development0.0387732940610384
GO:0004721phosphoprotein phosphatase activity0.0392051887455054
GO:0050769positive regulation of neurogenesis0.0405101214388895
GO:0007612learning0.0414980733231299
GO:0048513organ development0.0442590823351491
GO:0030282bone mineralization0.0442590823351491
GO:0032501multicellular organismal process0.0442590823351491
GO:0007026negative regulation of microtubule depolymerization0.0442590823351491
GO:0031114regulation of microtubule depolymerization0.0442590823351491
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0442590823351491
GO:0007019microtubule depolymerization0.0442590823351491
GO:0050794regulation of cellular process0.0442590823351491
GO:0050770regulation of axonogenesis0.0460191143005335
GO:0009953dorsal/ventral pattern formation0.0460191143005335
GO:0016791phosphoric monoester hydrolase activity0.0460191143005335
GO:0005887integral to plasma membrane0.0460191143005335
GO:0031110regulation of microtubule polymerization or depolymerization0.0460191143005335
GO:0019222regulation of metabolic process0.0460191143005335
GO:0008270zinc ion binding0.0460191143005335
GO:0031226intrinsic to plasma membrane0.0460191143005335
GO:0031109microtubule polymerization or depolymerization0.0484864686669324
GO:0004864protein phosphatase inhibitor activity0.0489067669941368



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>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.99e-14180
neural cell1.61e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system2.86e-4382
regional part of nervous system5.13e-4194
nervous system5.13e-4194
brain5.71e-3669
future brain5.71e-3669
neural tube1.07e-3457
neural rod1.07e-3457
future spinal cord1.07e-3457
neural keel1.07e-3457
ectoderm-derived structure2.30e-34169
head1.60e-33123
ectoderm1.71e-33173
presumptive ectoderm1.71e-33173
neural plate1.97e-3386
presumptive neural plate1.97e-3386
regional part of brain5.25e-3359
anterior region of body1.03e-32129
craniocervical region1.03e-32129
neurectoderm8.47e-3290
organism subdivision3.94e-29365
adult organism2.93e-28115
anterior neural tube3.57e-2642
regional part of forebrain4.27e-2641
forebrain4.27e-2641
future forebrain4.27e-2641
pre-chordal neural plate1.07e-2361
telencephalon4.54e-2234
gray matter5.55e-2234
brain grey matter5.55e-2234
regional part of telencephalon1.90e-2133
cerebral hemisphere5.12e-2132
multi-tissue structure3.14e-19347
multi-cellular organism1.19e-18659
cell layer1.09e-17312
cerebral cortex6.07e-1725
pallium6.07e-1725
epithelium7.57e-17309
anatomical cluster1.39e-16286
anatomical conduit1.80e-16241
anatomical system1.92e-15625
anatomical group3.58e-15626
tube4.95e-15194
regional part of cerebral cortex5.85e-1522
neocortex1.04e-1320
embryo1.92e-13612
organ3.72e-13511
embryonic structure1.66e-11605
developing anatomical structure1.66e-11605
germ layer3.38e-11604
embryonic tissue3.38e-11604
presumptive structure3.38e-11604
epiblast (generic)3.38e-11604
organ part1.68e-10219
posterior neural tube1.52e-0915
chordal neural plate1.52e-0915
segmental subdivision of nervous system4.28e-0813
segmental subdivision of hindbrain9.95e-0812
hindbrain9.95e-0812
presumptive hindbrain9.95e-0812


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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C361&oldid=1706497"