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Coexpression cluster:C3437: Difference between revisions

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|full_id=C3437_Whole_blood_Neutrophils_Eosinophils_parietal_occipital_breast
|full_id=C3437_Whole_blood_Neutrophils_Eosinophils_parietal_occipital_breast
|id=C3437
|id=C3437
|ontology_enrichment_celltype=CL:0000738!4.94e-15!140;CL:0000766!2.88e-12!76;CL:0000037!4.21e-12!172;CL:0000566!4.21e-12!172;CL:0002031!6.89e-12!124;CL:0002032!3.25e-11!165;CL:0000837!3.25e-11!165;CL:0000988!2.35e-10!182;CL:0002057!2.82e-10!42;CL:0002087!4.34e-10!119;CL:0000557!6.97e-10!71;CL:0000839!9.25e-10!70;CL:0000860!3.08e-09!45;CL:0000763!3.71e-09!112;CL:0000049!3.71e-09!112;CL:0002009!2.07e-08!65;CL:0002194!5.06e-08!63;CL:0000576!5.06e-08!63;CL:0000040!5.06e-08!63;CL:0000559!5.06e-08!63
|ontology_enrichment_celltype=CL:0000738!3.50e-16!136;CL:0000766!6.75e-13!72;CL:0002031!6.95e-13!120;CL:0000037!7.06e-13!168;CL:0000566!7.06e-13!168;CL:0002032!5.53e-12!161;CL:0000837!5.53e-12!161;CL:0002087!2.69e-11!115;CL:0000988!2.70e-11!177;CL:0000557!2.18e-10!67;CL:0000839!3.01e-10!66;CL:0000860!1.09e-09!42;CL:0002057!1.09e-09!42;CL:0000763!2.20e-09!108;CL:0000049!2.20e-09!108;CL:0000473!2.60e-09!48;CL:0000234!2.60e-09!48;CL:0002009!5.44e-09!61;CL:0002194!1.32e-08!59;CL:0000576!1.32e-08!59;CL:0000040!1.32e-08!59;CL:0000559!1.32e-08!59
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.90e-50!115;UBERON:0001049!2.75e-19!57;UBERON:0005068!2.75e-19!57;UBERON:0006241!2.75e-19!57;UBERON:0007135!2.75e-19!57;UBERON:0001017!8.01e-17!82;UBERON:0003080!3.38e-16!42;UBERON:0002616!3.43e-16!59;UBERON:0002780!1.05e-15!41;UBERON:0001890!1.05e-15!41;UBERON:0006240!1.05e-15!41;UBERON:0005743!2.09e-15!86;UBERON:0000955!3.24e-15!69;UBERON:0006238!3.24e-15!69;UBERON:0000073!3.64e-15!94;UBERON:0001016!3.64e-15!94;UBERON:0002020!5.82e-13!34;UBERON:0003528!5.82e-13!34;UBERON:0001893!6.35e-13!34;UBERON:0002390!1.58e-12!102;UBERON:0003061!1.58e-12!102;UBERON:0002619!2.27e-12!22;UBERON:0002791!2.30e-12!33;UBERON:0001869!3.49e-12!32;UBERON:0001950!1.47e-11!20;UBERON:0002346!2.13e-10!90;UBERON:0003075!2.22e-10!86;UBERON:0007284!2.22e-10!86;UBERON:0000956!3.99e-10!25;UBERON:0000203!3.99e-10!25;UBERON:0002193!1.26e-09!112;UBERON:0003056!1.45e-07!61;UBERON:0002371!1.88e-07!80;UBERON:0001474!4.18e-07!86;UBERON:0000178!5.05e-07!15;UBERON:0000179!5.05e-07!15;UBERON:0000463!5.05e-07!15
|ontology_enrichment_uberon=UBERON:0007023!9.05e-48!114;UBERON:0001049!1.46e-17!56;UBERON:0005068!1.46e-17!56;UBERON:0006241!1.46e-17!56;UBERON:0007135!1.46e-17!56;UBERON:0000073!1.92e-16!53;UBERON:0002616!1.92e-16!53;UBERON:0002780!1.43e-15!41;UBERON:0001890!1.43e-15!41;UBERON:0003080!1.43e-15!41;UBERON:0006240!1.43e-15!41;UBERON:0001017!7.35e-15!81;UBERON:0001016!2.13e-14!89;UBERON:0000955!1.88e-13!68;UBERON:0006238!1.88e-13!68;UBERON:0002390!4.11e-13!98;UBERON:0003061!4.11e-13!98;UBERON:0001893!5.05e-13!34;UBERON:0003528!6.32e-13!34;UBERON:0002020!6.32e-13!34;UBERON:0001869!1.99e-12!32;UBERON:0002619!3.59e-12!22;UBERON:0002791!4.68e-12!32;UBERON:0001950!1.31e-11!20;UBERON:0003075!1.03e-10!82;UBERON:0007284!1.03e-10!82;UBERON:0002346!1.92e-10!86;UBERON:0002193!3.84e-10!108;UBERON:0000956!4.49e-10!25;UBERON:0000203!4.49e-10!25;UBERON:0003056!2.96e-08!61;UBERON:0002371!9.82e-08!76;UBERON:0000178!1.21e-07!15;UBERON:0000179!1.21e-07!15;UBERON:0000463!1.21e-07!15;UBERON:0001474!2.37e-07!82
|tf_chipseq_enrich=BATF#10538;2:16.2385345282024:0.00491746240780997:0.0229962323203003!BCL11A#53335;2:18.9129700690714:0.00363940624837968:0.0183843264413313!BCLAF1#9774;2:14.4350984067479:0.00620114743554613:0.0273774787377833!BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296154850270892!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189627051127188!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00659446920716979!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032437297139723!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321269850660093!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319770290191232!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461065140673626!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167189740010122!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00760845712374825!FOSL2#2355;2:11.2868004030411:0.010053458697312:0.0376631455946827!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0153826759204207!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.01085219736627!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156441389530503!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.0324807675386513!MEF2C#4208;2:27.5409029950827:0.00172911993836969:0.0106465957577758!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293852402919788!NANOG#79923;2:19.4965189873418:0.00342725564850102:0.0174434284928751!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269087860405144!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470238558280152!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00880912724113185!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.0048383717709148!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245962024145436!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00628624480171383
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}}
}}

Revision as of 15:06, 19 October 2012


Full id: C3437_Whole_blood_Neutrophils_Eosinophils_parietal_occipital_breast



Phase1 CAGE Peaks

Hg19::chr14:60715908..60715926,+p2@PPM1A
Hg19::chr14:60715928..60716007,+p1@PPM1A
Hg19::chr5:10353780..10353890,+p1@MARCH6


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

No GOStat results

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
adult organism9.05e-48114
neural tube1.46e-1756
neural rod1.46e-1756
future spinal cord1.46e-1756
neural keel1.46e-1756
regional part of nervous system1.92e-1653
regional part of brain1.92e-1653
regional part of forebrain1.43e-1541
forebrain1.43e-1541
anterior neural tube1.43e-1541
future forebrain1.43e-1541
central nervous system7.35e-1581
nervous system2.13e-1489
brain1.88e-1368
future brain1.88e-1368
hematopoietic system4.11e-1398
blood island4.11e-1398
telencephalon5.05e-1334
brain grey matter6.32e-1334
gray matter6.32e-1334
cerebral hemisphere1.99e-1232
regional part of cerebral cortex3.59e-1222
regional part of telencephalon4.68e-1232
neocortex1.31e-1120
neural plate1.03e-1082
presumptive neural plate1.03e-1082
neurectoderm1.92e-1086
hemolymphoid system3.84e-10108
cerebral cortex4.49e-1025
pallium4.49e-1025
pre-chordal neural plate2.96e-0861
bone marrow9.82e-0876
blood1.21e-0715
haemolymphatic fluid1.21e-0715
organism substance1.21e-0715
bone element2.37e-0782


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#10538216.23853452820240.004917462407809970.0229962323203003
BCL11A#53335218.91297006907140.003639406248379680.0183843264413313
BCLAF1#9774214.43509840674790.006201147435546130.0273774787377833
BRCA1#672213.45615376214920.007119807716084560.0296154850270892
CCNT2#90536.336201576962630.003930750035764890.0189627051127188
CHD2#1106310.34402283411690.0009033701102746880.00659446920716979
E2F1#186934.907389214879320.008460985347239390.032437297139723
E2F6#187635.017155731697390.00791769806886330.0321269850660093
EGR1#195834.988179094810140.008056488137383440.0319770290191232
ELF1#199734.258097958807540.01295179875054610.0461065140673626
EP300#203336.77394172622320.003216880500103790.0167189740010122
ETS1#211339.728760922202340.001085840092584840.00760845712374825
FOSL2#2355211.28680040304110.0100534586973120.0376631455946827
GABPB1#255337.067683836182170.002832212825417420.0153826759204207
HMGN3#932438.178547723350590.001827766942164210.01085219736627
JUND#372736.994663941871030.002921845042734990.0156441389530503
MEF2A#4205212.4954872730960.008235029478029740.0324807675386513
MEF2C#4208227.54090299508270.001729119938369690.0106465957577758
MYC#460935.22228187160940.007020843755740150.0293852402919788
NANOG#79923219.49651898734180.003427255648501020.0174434284928751
NFKB1#479035.488063424193840.006049381815655430.0269087860405144
NRF1#4899312.21027944771090.0005492172401020010.00470238558280152
POU2F2#545239.106124057742520.001324165192682130.00880912724113185
RFX5#5993312.04791082719510.0005717246050312580.0048383717709148
SP1#666735.69838137814090.005403962701712170.0245962024145436
TCF12#6938310.63446490218640.0008313523990202070.00628624480171383



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.

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