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Coexpression cluster:C4351: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.019068400900425!CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000130093236680952!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326759918899654!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00438213160097995!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323557721412534!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321763504619575!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.046397506678613!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167992290889714!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764023805359211!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582931527185455!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.0010752232223758!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154582427631968!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388857165606365!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438105657871706!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000853032315404036!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392642981514152!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108974225993428!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123182904432259!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128491896867622!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270354481340767!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.0047252409044413!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00884292400783483!REST#5978;3:9.65002871612802:0.00111263624711459:0.00769808658578341!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00240135474297427!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.000721064546603812!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00616040869415852!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249031649616594!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00617719159973912!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330527932532191!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140637507113357!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.0039006737224716
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}}
}}

Revision as of 16:41, 26 November 2012


Full id: C4351_Reticulocytes_splenic_plasma_chronic_liver_optic_b



Phase1 CAGE Peaks

Hg19::chr3:98312434..98312474,-p1@CPOX
Hg19::chr3:98312478..98312489,-p3@CPOX
Hg19::chr3:98312500..98312515,-p2@CPOX


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural tube1.05e-1556
neural rod1.05e-1556
future spinal cord1.05e-1556
neural keel1.05e-1556
regional part of nervous system2.99e-1453
regional part of brain2.99e-1453
brain grey matter2.01e-1334
gray matter2.01e-1334
telencephalon2.27e-1334
brain6.75e-1368
future brain6.75e-1368
central nervous system1.87e-1281
regional part of telencephalon2.75e-1232
cerebral hemisphere3.81e-1232
regional part of forebrain2.16e-1141
forebrain2.16e-1141
anterior neural tube2.16e-1141
future forebrain2.16e-1141
neural plate6.45e-1182
presumptive neural plate6.45e-1182
nervous system1.27e-1089
structure with developmental contribution from neural crest2.30e-10132
neurectoderm1.04e-0986
regional part of cerebral cortex2.33e-0922
organ system subdivision2.49e-09223
cerebral cortex7.31e-0925
pallium7.31e-0925
neocortex1.24e-0820
ecto-epithelium1.25e-08104
adult organism1.37e-08114
tube2.64e-08192
anatomical conduit2.94e-08240
pre-chordal neural plate5.97e-0861
cell layer7.81e-08309
epithelium1.15e-07306
multi-tissue structure5.89e-07342


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
CCNT2#90536.336201576962630.003930750035764890.019068400900425
CTBP2#1488362.71700033932814.049570681927e-060.000130093236680952
E2F1#186934.907389214879320.008460985347239390.0326759918899654
E2F4#1874312.66806031528440.0004917987006298980.00438213160097995
E2F6#187635.017155731697390.00791769806886330.0323557721412534
EGR1#195834.988179094810140.008056488137383440.0321763504619575
ELF1#199734.258097958807540.01295179875054610.046397506678613
EP300#203336.77394172622320.003216880500103790.0167992290889714
ETS1#211339.728760922202340.001085840092584840.00764023805359211
FOXA1#3169311.08141974938550.000734755275698670.00582931527185455
FOXA2#3170324.63046375266526.68983856509345e-050.0010752232223758
GABPB1#255337.067683836182170.002832212825417420.0154582427631968
GATA1#2623313.56030814380040.0004009615963782630.00388857165606365
GATA2#2624312.7449317335540.0004829527704283790.00438105657871706
GATA3#2625327.2365163572064.94721007899563e-050.000853032315404036
HDAC2#3066313.41562023662630.0004140761399857210.00392642981514152
HMGN3#932438.178547723350590.001827766942164210.0108974225993428
HNF4A#3172323.13229036295378.07584663437677e-050.00123182904432259
IRF1#365937.63716375356390.002244692747297240.0128491896867622
NFKB1#479035.488063424193840.006049381815655430.0270354481340767
NRF1#4899312.21027944771090.0005492172401020010.0047252409044413
POU2F2#545239.106124057742520.001324165192682130.00884292400783483
REST#597839.650028716128020.001112636247114590.00769808658578341
SIX5#147912317.0867153554590.0002004060546325010.00240135474297427
TAL1#6886329.86861667744023.75103522793067e-050.000721064546603812
TCF7L2#6934310.77017656313730.0008003181298398380.00616040869415852
TFAP2A#7020316.5186343730450.0002218033880766340.00249031649616594
TFAP2C#7022310.80922860986020.0007916746575753130.00617719159973912
YY1#752834.911170749853860.008441455341808260.0330527932532191
ZBTB7A#5134137.35190930787590.002516255860282270.0140637507113357
ZNF143#7702313.50087655222790.0004062804962997170.0039006737224716



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.