Personal tools

Coexpression cluster:C1115

From FANTOM5_SSTAR

Revision as of 14:41, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1115_CD4_CD34_CD8_CD19_Basophils_Peripheral_Dendritic



Phase1 CAGE Peaks

Hg19::chr10:32667648..32667659,-p5@EPC1
Hg19::chr10:32667660..32667735,-p2@EPC1
Hg19::chr13:103249302..103249321,+p2@TPP2
Hg19::chr16:10479876..10479887,+p2@ATF7IP2
Hg19::chr2:242823508..242823531,+p1@ENST00000415434
p1@ENST00000430555
p1@ENST00000457686
Hg19::chr4:89205879..89205911,-p3@PPM1K
Hg19::chr9:100396030..100396055,+p3@NCBP1


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:0031442positive regulation of mRNA 3'-end processing0.00520005491694157
GO:0050685positive regulation of mRNA processing0.00520005491694157
GO:0004294tripeptidyl-peptidase II activity0.00520005491694157
GO:0008717D-alanyl-D-alanine endopeptidase activity0.00520005491694157
GO:0031974membrane-enclosed lumen0.00520005491694157
GO:0043233organelle lumen0.00520005491694157
GO:0051254positive regulation of RNA metabolic process0.00520005491694157
GO:0008240tripeptidyl-peptidase activity0.00520005491694157
GO:0031440regulation of mRNA 3'-end processing0.00520005491694157
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0112746726374699
GO:0000339RNA cap binding0.0133668470752712
GO:0031325positive regulation of cellular metabolic process0.0133668470752712
GO:0006379mRNA cleavage0.0133668470752712
GO:0050684regulation of mRNA processing0.0133668470752712
GO:0009893positive regulation of metabolic process0.0136880817127755
GO:0031124mRNA 3'-end processing0.0204607554870117
GO:0005654nucleoplasm0.0211322557389912
GO:0031123RNA 3'-end processing0.0233768379318203
GO:0051252regulation of RNA metabolic process0.0233768379318203
GO:0006406mRNA export from nucleus0.025709980262606
GO:0043170macromolecule metabolic process0.0273417798653032
GO:0045814negative regulation of gene expression, epigenetic0.0273417798653032
GO:0031981nuclear lumen0.0273417798653032
GO:0006405RNA export from nucleus0.0292021291118577
GO:0004289subtilase activity0.0323355491475181
GO:0015071protein phosphatase type 2C activity0.0323355491475181
GO:0051168nuclear export0.0380395566131108
GO:0044237cellular metabolic process0.0396635721962796
GO:0048522positive regulation of cellular process0.0396635721962796
GO:0044238primary metabolic process0.0396635721962796
GO:0044424intracellular part0.0413916159462054
GO:0008287protein serine/threonine phosphatase complex0.0415469369327996
GO:0048518positive regulation of biological process0.0432967094918313
GO:0040029regulation of gene expression, epigenetic0.0432967094918313
GO:0004722protein serine/threonine phosphatase activity0.0432967094918313
GO:0044428nuclear part0.043958325953636
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0472815342760447
GO:0051028mRNA transport0.0475876790435889
GO:0043283biopolymer metabolic process0.0475876790435889
GO:0004177aminopeptidase activity0.0475876790435889
GO:0031323regulation of cellular metabolic process0.0475876790435889
GO:0050658RNA transport0.0475876790435889
GO:0051236establishment of RNA localization0.0475876790435889
GO:0050657nucleic acid transport0.0475876790435889
GO:0006403RNA localization0.0475876790435889
GO:0044446intracellular organelle part0.0483810973952469
GO:0044422organelle part0.0483810973952469
GO:0019222regulation of metabolic process0.0483810973952469
GO:0016070RNA metabolic process0.0483810973952469
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0483810973952469



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism2.92e-24114
neural tube1.45e-1456
neural rod1.45e-1456
future spinal cord1.45e-1456
neural keel1.45e-1456
regional part of nervous system8.03e-1453
regional part of brain8.03e-1453
nervous system1.58e-1389
central nervous system5.09e-1381
regional part of forebrain6.11e-1341
forebrain6.11e-1341
anterior neural tube6.11e-1341
future forebrain6.11e-1341
brain1.05e-1168
future brain1.05e-1168
telencephalon1.49e-1034
brain grey matter1.55e-1034
gray matter1.55e-1034
cerebral hemisphere1.94e-1032
regional part of telencephalon2.90e-1032
neurectoderm1.39e-0886
regional part of cerebral cortex2.03e-0822
cerebral cortex3.60e-0825
pallium3.60e-0825
neocortex6.66e-0820
neural plate8.32e-0882
presumptive neural plate8.32e-0882
blood1.73e-0715
haemolymphatic fluid1.73e-0715
organism substance1.73e-0715
Disease
Ontology termp-valuen
hematologic cancer2.51e-0751
immune system cancer2.51e-0751


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CHD2#110657.38858773865490.0001498689600820670.00193141218188685
E2F1#186953.505278010628090.005090553587915050.0236837280010807
E2F4#187435.429168706550470.01350675082176140.0477032075030923
EGR1#195853.562985067721530.004722351211058930.0222552068106937
ELF1#199753.041498542005380.009719562269370750.0365565169926106
EP300#203343.870823843556110.01142567586684480.041859408631473
FOS#235345.141688747939660.004042095865678250.0193479284163147
GTF2B#2959418.25361710532813.11241110089347e-050.0006292239701243
GTF2F1#296235.459854661467560.0132988216841570.0470213161985129
HEY1#2346263.462952322662040.001267890095872120.00850354313657776
IRF1#365944.364093573465090.00739345582427820.0305493405931236
NANOG#79923312.53347649186260.001261052189503470.00846747007969353
NFKB1#479053.92004530299560.003036581424484610.0161155306363
NFYA#4800615.7933548855691.7032585757508e-079.38220582240704e-06
NFYB#4801614.36553707445982.99325254948281e-071.50947514734638e-05
PAX5#507943.811180303530190.01208261681555190.0438204124596112
POLR2A#543072.147453176558070.004747636447610280.0223219917594188
REST#597856.892877654377160.0002094388584846510.00243825492601477
RFX5#5993610.32678070902442.12421369818918e-067.73538195345816e-05
SP1#666764.884326895549340.0001736361122290910.00211282557673238
SP2#6668414.94487456791126.81071539656055e-050.00108762126192873
TAF1#687262.865468244924540.003728330207471460.0185818696510671
TBP#690863.177232017511190.002074112051852660.0120149863322114
TCF7L2#693446.154386607507050.002064676148138040.0119689560521419
TRIM28#1015537.967367876541080.004622341263156460.0218311716719937
YY1#752853.507979107038470.005072570672808980.0236095284325281



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:C1115&oldid=2557451"