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Coexpression cluster:C2564: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.00e-25!57;UBERON:0005068!1.00e-25!57;UBERON:0006241!1.00e-25!57;UBERON:0007135!1.00e-25!57;UBERON:0002390!1.92e-25!102;UBERON:0003061!1.92e-25!102;UBERON:0001017!5.24e-25!82;UBERON:0002193!8.94e-24!112;UBERON:0005743!2.85e-23!86;UBERON:0002371!3.49e-23!80;UBERON:0002616!1.32e-22!59;UBERON:0001474!9.19e-22!86;UBERON:0000073!1.68e-21!94;UBERON:0001016!1.68e-21!94;UBERON:0000955!2.35e-20!69;UBERON:0006238!2.35e-20!69;UBERON:0002780!2.24e-19!41;UBERON:0001890!2.24e-19!41;UBERON:0006240!2.24e-19!41;UBERON:0003080!3.89e-19!42;UBERON:0004765!1.30e-18!101;UBERON:0001434!1.30e-18!101;UBERON:0002020!1.24e-17!34;UBERON:0003528!1.24e-17!34;UBERON:0001893!1.51e-17!34;UBERON:0007023!3.27e-17!115;UBERON:0002791!4.85e-17!33;UBERON:0002346!7.63e-17!90;UBERON:0003075!9.62e-17!86;UBERON:0007284!9.62e-17!86;UBERON:0001869!2.58e-16!32;UBERON:0002405!1.15e-12!115;UBERON:0000956!1.64e-12!25;UBERON:0000203!1.64e-12!25;UBERON:0002619!1.93e-12!22;UBERON:0003056!2.25e-12!61;UBERON:0001950!2.20e-11!20;UBERON:0000153!1.02e-08!129;UBERON:0007811!1.02e-08!129;UBERON:0000033!1.73e-08!123;UBERON:0003076!9.18e-08!15;UBERON:0003057!9.18e-08!15;UBERON:0002204!1.84e-07!167;UBERON:0004732!9.32e-07!13
|ontology_enrichment_uberon=UBERON:0001049!1.00e-25!57;UBERON:0005068!1.00e-25!57;UBERON:0006241!1.00e-25!57;UBERON:0007135!1.00e-25!57;UBERON:0002390!1.92e-25!102;UBERON:0003061!1.92e-25!102;UBERON:0001017!5.24e-25!82;UBERON:0002193!8.94e-24!112;UBERON:0005743!2.85e-23!86;UBERON:0002371!3.49e-23!80;UBERON:0002616!1.32e-22!59;UBERON:0001474!9.19e-22!86;UBERON:0000073!1.68e-21!94;UBERON:0001016!1.68e-21!94;UBERON:0000955!2.35e-20!69;UBERON:0006238!2.35e-20!69;UBERON:0002780!2.24e-19!41;UBERON:0001890!2.24e-19!41;UBERON:0006240!2.24e-19!41;UBERON:0003080!3.89e-19!42;UBERON:0004765!1.30e-18!101;UBERON:0001434!1.30e-18!101;UBERON:0002020!1.24e-17!34;UBERON:0003528!1.24e-17!34;UBERON:0001893!1.51e-17!34;UBERON:0007023!3.27e-17!115;UBERON:0002791!4.85e-17!33;UBERON:0002346!7.63e-17!90;UBERON:0003075!9.62e-17!86;UBERON:0007284!9.62e-17!86;UBERON:0001869!2.58e-16!32;UBERON:0002405!1.15e-12!115;UBERON:0000956!1.64e-12!25;UBERON:0000203!1.64e-12!25;UBERON:0002619!1.93e-12!22;UBERON:0003056!2.25e-12!61;UBERON:0001950!2.20e-11!20;UBERON:0000153!1.02e-08!129;UBERON:0007811!1.02e-08!129;UBERON:0000033!1.73e-08!123;UBERON:0003076!9.18e-08!15;UBERON:0003057!9.18e-08!15;UBERON:0002204!1.84e-07!167;UBERON:0004732!9.32e-07!13
|tf_chipseq_enrich=BATF#10538;3:18.2683513442277:0.000268166010572129:0.00286721846623081!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997319412050402!EP300#2033;3:5.0804562946674:0.0114429840539824:0.0418978338106109!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00194987026327262!GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0109010813978778!GTF2B#2959;3:23.9578724507432:0.000119775456285592:0.00162457517909233!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0320105447644645!JUN#3725;3:9.38462189425225:0.00191899450203047:0.0112860607499471!JUNB#3726;3:22.9579744948659:0.000135977250401878:0.00177916913739937!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386957862225173!RXRA#6256;2:10.0373085695666:0.0139170380592011:0.0488811682483573!STAT3#6774;3:7.88959874786568:0.00319076048168013:0.0167423550013159!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244420663072009!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483074308252149!USF2#7392;3:9.7441480388022:0.00171834184841007:0.010721184318424
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}}
}}

Revision as of 12:01, 5 September 2012


Full id: C2564_optic_CD14_spinal_corpus_thalamus_substantia_locus



Phase1 CAGE Peaks

Hg19::chr1:212732307..212732355,-p1@uc001hje.2
Hg19::chr4:56261764..56261833,+p3@TMEM165
Hg19::chr6:161695042..161695064,-p2@AGPAT4
Hg19::chr6:161695074..161695112,-p1@AGPAT4


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:00038411-acylglycerol-3-phosphate O-acyltransferase activity0.0103591865847246
GO:0016411acylglycerol O-acyltransferase activity0.0103591865847246
GO:0008374O-acyltransferase activity0.0151029214517312
GO:0008654phospholipid biosynthetic process0.0292229120021243
GO:0046467membrane lipid biosynthetic process0.0292229120021243
GO:0006644phospholipid metabolic process0.0381709954969072
GO:0008415acyltransferase activity0.0381709954969072
GO:0016747transferase activity, transferring groups other than amino-acyl groups0.0381709954969072
GO:0006643membrane lipid metabolic process0.0381709954969072
GO:0016746transferase activity, transferring acyl groups0.0381709954969072
GO:0008610lipid biosynthetic process0.0390171657311839



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>


Uber Anatomy
Ontology termp-valuen
neural tube1.00e-2557
neural rod1.00e-2557
future spinal cord1.00e-2557
neural keel1.00e-2557
hematopoietic system1.92e-25102
blood island1.92e-25102
central nervous system5.24e-2582
hemolymphoid system8.94e-24112
bone marrow3.49e-2380
regional part of brain1.32e-2259
bone element9.19e-2286
regional part of nervous system1.68e-2194
nervous system1.68e-2194
brain2.35e-2069
future brain2.35e-2069
regional part of forebrain2.24e-1941
forebrain2.24e-1941
future forebrain2.24e-1941
anterior neural tube3.89e-1942
skeletal element1.30e-18101
skeletal system1.30e-18101
gray matter1.24e-1734
brain grey matter1.24e-1734
telencephalon1.51e-1734
adult organism3.27e-17115
regional part of telencephalon4.85e-1733
neurectoderm7.63e-1790
neural plate9.62e-1786
presumptive neural plate9.62e-1786
cerebral hemisphere2.58e-1632
immune system1.15e-12115
cerebral cortex1.64e-1225
pallium1.64e-1225
regional part of cerebral cortex1.93e-1222
pre-chordal neural plate2.25e-1261
neocortex2.20e-1120
anterior region of body1.02e-08129
craniocervical region1.02e-08129
head1.73e-08123
posterior neural tube9.18e-0815
chordal neural plate9.18e-0815
musculoskeletal system1.84e-07167
segmental subdivision of nervous system9.32e-0713


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
BATF#10538318.26835134422770.0002681660105721290.00286721846623081
E2F6#187645.017155731697390.00157802193473060.00997319412050402
EP300#203335.08045629466740.01144298405398240.0418978338106109
FOS#235348.99795530889440.0001525147711168630.00194987026327262
GATA2#262439.55869880016550.001818151618357440.0109010813978778
GTF2B#2959323.95787245074320.0001197754562855920.00162457517909233
IRF1#365935.727872815172930.008097114790333330.0320105447644645
JUN#372539.384621894252250.001918994502030470.0112860607499471
JUNB#3726322.95797449486590.0001359772504018780.00177916913739937
JUND#372735.245997956403270.01043432751748420.0386957862225173
RXRA#6256210.03730856956660.01391703805920110.0488811682483573
STAT3#677437.889598747865680.003190760481680130.0167423550013159
TBP#690843.706770687096390.005296377814784350.0244420663072009
USF1#739134.771124457905970.01370465887188020.0483074308252149
USF2#739239.74414803880220.001718341848410070.010721184318424



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.