Personal tools

Coexpression cluster:C291

From FANTOM5_SSTAR

Revision as of 18:43, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C291_spinal_substantia_retina_medulla_tongue_skeletal_trachea



Phase1 CAGE Peaks

Hg19::chr10:104184955..104184965,-p4@CUEDC2
Hg19::chr10:60936793..60936819,-p@chr10:60936793..60936819
-
Hg19::chr11:125366211..125366212,-p14@FEZ1
Hg19::chr17:42984119..42984130,-p43@GFAP
Hg19::chr17:42984138..42984151,-p38@GFAP
Hg19::chr17:42984459..42984521,+p@chr17:42984459..42984521
+
Hg19::chr17:42984550..42984567,+p@chr17:42984550..42984567
+
Hg19::chr17:42984604..42984618,+p@chr17:42984604..42984618
+
Hg19::chr17:42989173..42989181,-p40@GFAP
Hg19::chr17:73504580..73504588,-p@chr17:73504580..73504588
-
Hg19::chr19:1452223..1452232,+p@chr19:1452223..1452232
+
Hg19::chr19:40919278..40919294,-p2@PRX
Hg19::chr1:156404868..156404881,+p@chr1:156404868..156404881
+
Hg19::chr1:156404895..156404923,+p@chr1:156404895..156404923
+
Hg19::chr1:156404975..156404990,+p@chr1:156404975..156404990
+
Hg19::chr1:161275051..161275059,-p@chr1:161275051..161275059
-
Hg19::chr1:161275062..161275086,-p@chr1:161275062..161275086
-
Hg19::chr1:161275096..161275109,-p@chr1:161275096..161275109
-
Hg19::chr1:161275111..161275127,-p@chr1:161275111..161275127
-
Hg19::chr1:161275189..161275203,-p@chr1:161275189..161275203
-
Hg19::chr1:161275238..161275250,-p@chr1:161275238..161275250
-
Hg19::chr1:161275265..161275277,-p@chr1:161275265..161275277
-
Hg19::chr1:161275395..161275412,-p@chr1:161275395..161275412
-
Hg19::chr1:161275623..161275644,-p@chr1:161275623..161275644
-
Hg19::chr1:161276191..161276202,-p6@MPZ
Hg19::chr1:161276686..161276694,-p11@MPZ
Hg19::chr1:161279749..161279764,-p1@MPZ
Hg19::chr1:44991346..44991355,+p@chr1:44991346..44991355
+
Hg19::chr20:52573198..52573199,-p@chr20:52573198..52573199
-
Hg19::chr2:128403624..128403631,+p4@GPR17
Hg19::chr2:128403720..128403732,+p1@GPR17
Hg19::chr2:241521605..241521654,-p@chr2:241521605..241521654
-
Hg19::chr3:44062980..44062993,+p@chr3:44062980..44062993
+
Hg19::chr4:115519490..115519496,+p11@UGT8
Hg19::chr5:123774243..123774262,-p@chr5:123774243..123774262
-
Hg19::chr5:123774265..123774292,-p@chr5:123774265..123774292
-
Hg19::chr5:123774307..123774326,-p@chr5:123774307..123774326
-
Hg19::chr5:146435694..146435705,-p23@PPP2R2B
Hg19::chr6:133424178..133424190,-p@chr6:133424178..133424190
-
Hg19::chr7:29966288..29966313,-p@chr7:29966288..29966313
-
Hg19::chr7:33842781..33842787,-p1@ENST00000440034
Hg19::chr7:4998664..4998674,-p2@MMD2
Hg19::chr7:99531868..99531881,-p@chr7:99531868..99531881
-
Hg19::chr9:90113407..90113437,+p11@DAPK1


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:0007638mechanosensory behavior0.000225625857182879
GO:0032502developmental process0.000680714741513836
GO:0009612response to mechanical stimulus0.000680714741513836
GO:0007422peripheral nervous system development0.00103494969512009
GO:0007399nervous system development0.00143356170058839
GO:0008489UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity0.00754747717880883
GO:00038512-hydroxyacylsphingosine 1-beta-galactosyltransferase activity0.00754747717880883
GO:0048468cell development0.00754747717880883
GO:0048731system development0.0170389325473447
GO:0045217intercellular junction maintenance0.0170389325473447
GO:0009628response to abiotic stimulus0.0180450614628599
GO:0048869cellular developmental process0.0193185416021582
GO:0030154cell differentiation0.0193185416021582
GO:0048856anatomical structure development0.0239334495934795
GO:0008219cell death0.0239334495934795
GO:0016265death0.0239334495934795
GO:0043015gamma-tubulin binding0.0267100411830768
GO:0006688glycosphingolipid biosynthetic process0.0309604441808687
GO:0007275multicellular organismal development0.0309604441808687
GO:0007610behavior0.0309604441808687
GO:0019226transmission of nerve impulse0.0369535581590065
GO:0009247glycolipid biosynthetic process0.038663346172115
GO:0019835cytolysis0.0394425961671539
GO:0035250UDP-galactosyltransferase activity0.0401562837425331
GO:0045216intercellular junction assembly and maintenance0.0408122765299571
GO:0006687glycosphingolipid metabolic process0.0414172317562238
GO:0030148sphingolipid biosynthetic process0.0440698256137007
GO:0005856cytoskeleton0.0468734084861649
GO:0007028cytoplasm organization and biogenesis0.0468734084861649



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism4.35e-44115
central nervous system7.97e-3482
neural tube1.27e-3357
neural rod1.27e-3357
future spinal cord1.27e-3357
neural keel1.27e-3357
regional part of nervous system5.63e-3294
nervous system5.63e-3294
regional part of brain1.61e-3059
brain5.57e-2769
future brain5.57e-2769
anterior neural tube1.86e-2642
regional part of forebrain4.77e-2641
forebrain4.77e-2641
future forebrain4.77e-2641
neural plate1.40e-2286
presumptive neural plate1.40e-2286
gray matter2.15e-2234
brain grey matter2.15e-2234
telencephalon2.18e-2234
neurectoderm4.06e-2290
regional part of telencephalon9.87e-2233
cerebral hemisphere6.02e-2132
ectoderm-derived structure3.57e-17169
ectoderm3.87e-17173
presumptive ectoderm3.87e-17173
cerebral cortex1.59e-1625
pallium1.59e-1625
pre-chordal neural plate3.57e-1661
regional part of cerebral cortex3.50e-1522
anterior region of body4.78e-14129
craniocervical region4.78e-14129
neocortex6.22e-1420
head1.77e-13123
embryo4.19e-09612
posterior neural tube2.68e-0815
chordal neural plate2.68e-0815
anatomical conduit2.20e-07241
embryonic structure2.28e-07605
developing anatomical structure2.28e-07605
nucleus of brain2.48e-079
neural nucleus2.48e-079
basal ganglion3.31e-079
nuclear complex of neuraxis3.31e-079
aggregate regional part of brain3.31e-079
collection of basal ganglia3.31e-079
cerebral subcortex3.31e-079
germ layer3.94e-07604
embryonic tissue3.94e-07604
presumptive structure3.94e-07604
epiblast (generic)3.94e-07604
tube3.98e-07194
segmental subdivision of nervous system6.64e-0713
multi-cellular organism7.62e-07659
brainstem8.37e-078


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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C291&oldid=1990855"