Personal tools

Coexpression cluster:C552

From FANTOM5_SSTAR

Revision as of 18:09, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C552_medial_temporal_occipital_parietal_duodenum_brain_spinal



Phase1 CAGE Peaks

Hg19::chr10:105048252..105048262,+p@chr10:105048252..105048262
+
Hg19::chr10:105048347..105048358,+p@chr10:105048347..105048358
+
Hg19::chr11:132289875..132289896,-p12@OPCML
Hg19::chr16:7568144..7568155,+p@chr16:7568144..7568155
+
Hg19::chr17:44039779..44039792,+p6@MAPT
Hg19::chr17:44068857..44068869,+p8@MAPT
Hg19::chr2:149633261..149633270,+p1@AB384491
Hg19::chr2:50148868..50148876,-p32@NRXN1
Hg19::chr2:55253343..55253360,-p29@RTN4
Hg19::chr3:286287..286329,+p@chr3:286287..286329
+
Hg19::chr3:383640..383650,+p@chr3:383640..383650
+
Hg19::chr5:71482490..71482501,+p@chr5:71482490..71482501
+
Hg19::chr5:71482533..71482549,+p@chr5:71482533..71482549
+
Hg19::chr5:71489693..71489706,+p@chr5:71489693..71489706
+
Hg19::chr8:80567211..80567218,+p9@STMN2
Hg19::chr9:111911992..111912002,-p@chr9:111911992..111912002
-


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:0030516regulation of axon extension0.00010362994502982
GO:0030182neuron differentiation0.00010362994502982
GO:0048675axon extension0.00010362994502982
GO:0030426growth cone0.00010362994502982
GO:0030427site of polarized growth0.00010362994502982
GO:0048699generation of neurons0.00010362994502982
GO:0022008neurogenesis0.000112726089605561
GO:0050770regulation of axonogenesis0.000123735069240019
GO:0050767regulation of neurogenesis0.000237741650507623
GO:0007399nervous system development0.00158975368646609
GO:0007409axonogenesis0.00166359731717786
GO:0048667neuron morphogenesis during differentiation0.00166359731717786
GO:0048812neurite morphogenesis0.00166359731717786
GO:0000904cellular morphogenesis during differentiation0.00170318642141137
GO:0031175neurite development0.00182484678637508
GO:0048666neuron development0.00222579120033241
GO:0045298tubulin complex0.00304731298129318
GO:0032990cell part morphogenesis0.0031203738849544
GO:0048858cell projection morphogenesis0.0031203738849544
GO:0030030cell projection organization and biogenesis0.0031203738849544
GO:0019987negative regulation of anti-apoptosis0.00347582725292053
GO:0030517negative regulation of axon extension0.00347582725292053
GO:0048468cell development0.00347582725292053
GO:0050793regulation of developmental process0.00347582725292053
GO:0042995cell projection0.00575468023354051
GO:0045773positive regulation of axon extension0.00575468023354051
GO:0050771negative regulation of axonogenesis0.00575468023354051
GO:0048731system development0.00615746870355665
GO:0031116positive regulation of microtubule polymerization0.0062504053506897
GO:0031112positive regulation of microtubule polymerization or depolymerization0.00668206759859369
GO:0031113regulation of microtubule polymerization0.00668206759859369
GO:0005515protein binding0.00719152808698763
GO:0048869cellular developmental process0.00720625871783252
GO:0030154cell differentiation0.00720625871783252
GO:0046785microtubule polymerization0.00739713234206427
GO:0008038neuron recognition0.00791035634833841
GO:0050768negative regulation of neurogenesis0.00795198723378637
GO:0045767regulation of anti-apoptosis0.00795198723378637
GO:0048856anatomical structure development0.00795198723378637
GO:0050772positive regulation of axonogenesis0.00795198723378637
GO:0000902cell morphogenesis0.00795198723378637
GO:0032989cellular structure morphogenesis0.00795198723378637
GO:0016020membrane0.00795198723378637
GO:0051130positive regulation of cellular component organization and biogenesis0.00805275855365829
GO:0004985opioid receptor activity0.00805275855365829
GO:0050769positive regulation of neurogenesis0.00900202403800668
GO:0007275multicellular organismal development0.0104480426339578
GO:0017124SH3 domain binding0.0107811353522219
GO:0007026negative regulation of microtubule depolymerization0.0113835384307388
GO:0031114regulation of microtubule depolymerization0.0113835384307388
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0114425685972422
GO:0007019microtubule depolymerization0.0114425685972422
GO:0031110regulation of microtubule polymerization or depolymerization0.0138883244812153
GO:0008034lipoprotein binding0.0138883244812153
GO:0031109microtubule polymerization or depolymerization0.0150437531143522
GO:0030424axon0.0156967109218176
GO:0008037cell recognition0.0172315456118835
GO:0051261protein depolymerization0.020489944257951
GO:0008017microtubule binding0.0214525192020646
GO:0022610biological adhesion0.0216605349071122
GO:0007155cell adhesion0.0216605349071122
GO:0051129negative regulation of cellular component organization and biogenesis0.0216605349071122
GO:0030176integral to endoplasmic reticulum membrane0.0217253746280847
GO:0032502developmental process0.0225500834866176
GO:0030334regulation of cell migration0.0235007884009187
GO:0009653anatomical structure morphogenesis0.0235007884009187
GO:0031227intrinsic to endoplasmic reticulum membrane0.0235007884009187
GO:0015631tubulin binding0.0254237655144738
GO:0051094positive regulation of developmental process0.0254277678098717
GO:0051270regulation of cell motility0.0254316124385206
GO:0048523negative regulation of cellular process0.0257941112672204
GO:0040012regulation of locomotion0.0257941112672204
GO:0040011locomotion0.0257941112672204
GO:0048519negative regulation of biological process0.0264757184329733
GO:0051093negative regulation of developmental process0.0264757184329733
GO:0043005neuron projection0.0272872935115342
GO:0032501multicellular organismal process0.0272872935115342
GO:0005200structural constituent of cytoskeleton0.0280891153272492
GO:0051258protein polymerization0.0316265304462711
GO:0051128regulation of cellular component organization and biogenesis0.0321914258461296
GO:0000226microtubule cytoskeleton organization and biogenesis0.0324260624446285
GO:0051248negative regulation of protein metabolic process0.0326548287373963
GO:0048503GPI anchor binding0.038874450927321
GO:0019904protein domain specific binding0.038874450927321
GO:0031301integral to organelle membrane0.042017371296162
GO:0001653peptide receptor activity0.0436863081765911
GO:0008528peptide receptor activity, G-protein coupled0.0436863081765911
GO:0031300intrinsic to organelle membrane0.0443467218518709
GO:0006916anti-apoptosis0.0489890794507065



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 cell7.99e-12180
fibroblast3.78e-0775
Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.93e-3794
nervous system4.93e-3794
central nervous system6.36e-3782
neural tube8.78e-3357
neural rod8.78e-3357
future spinal cord8.78e-3357
neural keel8.78e-3357
brain3.03e-3069
future brain3.03e-3069
regional part of brain1.68e-2859
neurectoderm5.28e-2890
neural plate9.15e-2786
presumptive neural plate9.15e-2786
anterior neural tube1.13e-2642
regional part of forebrain3.00e-2641
forebrain3.00e-2641
future forebrain3.00e-2641
ectoderm1.06e-25173
presumptive ectoderm1.06e-25173
ectoderm-derived structure1.78e-24169
gray matter1.62e-2234
brain grey matter1.62e-2234
telencephalon2.47e-2234
regional part of telencephalon1.04e-2133
head1.40e-21123
cerebral hemisphere2.86e-2132
pre-chordal neural plate3.38e-2061
anterior region of body4.40e-20129
craniocervical region4.40e-20129
adult organism3.14e-18115
organism subdivision5.60e-18365
cerebral cortex4.57e-1725
pallium4.57e-1725
regional part of cerebral cortex6.57e-1622
tube7.30e-15194
neocortex1.31e-1420
anatomical conduit3.56e-14241
epithelium1.26e-13309
cell layer1.91e-13312
anatomical cluster1.83e-12286
multi-cellular organism1.20e-11659
anatomical system6.07e-08625
multi-tissue structure6.19e-08347
anatomical group7.23e-08626
embryo9.64e-08612
posterior neural tube2.17e-0715
chordal neural plate2.17e-0715
basal ganglion6.62e-079
nuclear complex of neuraxis6.62e-079
aggregate regional part of brain6.62e-079
collection of basal ganglia6.62e-079
cerebral subcortex6.62e-079
nucleus of brain6.75e-079
neural nucleus6.75e-079


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:C552&oldid=2139903"