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Coexpression cluster:C3763: Difference between revisions

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|tf_chipseq_enrich=BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.00139186916839092!BRCA1#672;3:20.1842306432238:0.000121570486027164:0.00164188542482749!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189969274865918!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325280441979067!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00436945678392905!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322108315913841!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320525528391371!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462152075475173!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00761919197994274!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243010237939!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154051078211432!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00387884662506015!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00433751954332594!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391222163777535!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108670244604741!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128021770333648!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00136566434310324!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444117165308172!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156730649418695!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.0072013751352206!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294406930460831!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269558574727041!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00199507141167348!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308953050894629!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172857546390656!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136585237344099!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00881980156623271!REST#5978;3:9.65002871612802:0.00111263624711459:0.00767317861941367!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484425977809991!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276637353294541!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00202997608508478!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308993924295291!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024639153959841!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00374984971401194!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00154855839545!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613553733849687!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615924534881616!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000646852093031887!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197022159840014!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190211625899694!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329281076582921!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140142515887382!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109397582848428
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}}
}}

Revision as of 16:20, 26 November 2012


Full id: C3763_occipital_brain_parietal_temporal_locus_cerebellum_spinal



Phase1 CAGE Peaks

Hg19::chr19:17445541..17445602,-p1@ANO8
Hg19::chr19:17445613..17445648,-p2@ANO8
Hg19::chr19:17445653..17445673,-p3@ANO8


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
nervous system2.17e-3489
central nervous system4.63e-3481
neural tube7.48e-3156
neural rod7.48e-3156
future spinal cord7.48e-3156
neural keel7.48e-3156
regional part of nervous system8.44e-2953
regional part of brain8.44e-2953
brain1.26e-2868
future brain1.26e-2868
neurectoderm2.73e-2686
neural plate1.09e-2482
presumptive neural plate1.09e-2482
regional part of forebrain3.16e-2241
forebrain3.16e-2241
anterior neural tube3.16e-2241
future forebrain3.16e-2241
brain grey matter9.21e-2134
gray matter9.21e-2134
telencephalon1.68e-2034
ectoderm-derived structure2.67e-20171
ectoderm2.67e-20171
presumptive ectoderm2.67e-20171
regional part of telencephalon1.75e-1932
cerebral hemisphere2.01e-1932
pre-chordal neural plate7.13e-1861
ecto-epithelium1.55e-17104
structure with developmental contribution from neural crest3.30e-16132
organ system subdivision5.73e-16223
cerebral cortex2.40e-1525
pallium2.40e-1525
regional part of cerebral cortex8.20e-1522
adult organism5.82e-14114
neocortex1.38e-1320
posterior neural tube1.00e-0915
chordal neural plate1.00e-0915
segmental subdivision of nervous system3.10e-0813
anatomical cluster7.06e-08373
segmental subdivision of hindbrain8.68e-0812
hindbrain8.68e-0812
presumptive hindbrain8.68e-0812
organ part5.42e-07218
neural nucleus6.93e-079
nucleus of brain6.93e-079
basal ganglion7.20e-079
nuclear complex of neuraxis7.20e-079
aggregate regional part of brain7.20e-079
collection of basal ganglia7.20e-079
cerebral subcortex7.20e-079


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
BCLAF1#9774321.65264761012189.8473954032885e-050.00139186916839092
BRCA1#672320.18423064322380.0001215704860271640.00164188542482749
CCNT2#90536.336201576962630.003930750035764890.0189969274865918
E2F1#186934.907389214879320.008460985347239390.0325280441979067
E2F4#1874312.66806031528440.0004917987006298980.00436945678392905
E2F6#187635.017155731697390.00791769806886330.0322108315913841
EGR1#195834.988179094810140.008056488137383440.0320525528391371
ELF1#199734.258097958807540.01295179875054610.0462152075475173
ETS1#211339.728760922202340.001085840092584840.00761919197994274
FOSL2#2355316.93020060456170.0002060162053171620.00243010237939
GABPB1#255337.067683836182170.002832212825417420.0154051078211432
GATA1#2623313.56030814380040.0004009615963782630.00387884662506015
GTF2F1#2962312.73966087675770.0004835525047438590.00433751954332594
HDAC2#3066313.41562023662630.0004140761399857210.00391222163777535
HMGN3#932438.178547723350590.001827766942164210.0108670244604741
IRF1#365937.63716375356390.002244692747297240.0128021770333648
IRF4#3662321.91451268674419.49854535978121e-050.00136566434310324
JUN#3725312.51282919233630.0005103313992726250.00444117165308172
JUND#372736.994663941871030.002921845042734990.0156730649418695
MXI1#460139.96157162875930.001011470541259020.0072013751352206
MYC#460935.22228187160940.007020843755740150.0294406930460831
NFKB1#479035.488063424193840.006049381815655430.0269558574727041
NFYA#4800318.42558069983050.0001598135507814160.00199507141167348
NR3C1#2908314.9730233311730.0002978331194675480.00308953050894629
PAX5#507936.669565531177830.003370290999677260.0172857546390656
PBX3#5090321.91451268674419.49854535978121e-050.00136585237344099
POU2F2#545239.106124057742520.001324165192682130.00881980156623271
REST#597839.650028716128020.001112636247114590.00767317861941367
RFX5#5993312.04791082719510.0005717246050312580.00484425977809991
SIN3A#2594235.408884726815140.006318961977991520.0276637353294541
SMARCB1#6598318.25271578115740.000164397760679890.00202997608508478
SMC3#9126315.04493284493280.0002935825420371870.00308993924295291
SP1#666735.69838137814090.005403962701712170.024639153959841
SRF#6722313.79717826216780.0003806615025800190.00374984971401194
STAT1#6772320.70658749719920.0001125992441046670.00154855839545
TCF7L2#6934310.77017656313730.0008003181298398380.00613553733849687
TFAP2C#7022310.80922860986020.0007916746575753130.00615924534881616
THAP1#55145331.36914460285133.23800758564397e-050.000646852093031887
TRIM28#10155318.59052504526250.0001555969297255280.00197022159840014
USF1#739136.361499277207960.00388404057290560.0190211625899694
YY1#752834.911170749853860.008441455341808260.0329281076582921
ZBTB7A#5134137.35190930787590.002516255860282270.0140142515887382
ZNF263#1012738.221841637010680.001799043925565870.0109397582848428



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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