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Coexpression cluster:C3517: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189688385077742!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279018670829452!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171494465521384!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00436462988571431!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321469684179145!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319904024249179!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461269534427377!ELK4#2005;3:16.235681658468:0.000233604395574599:0.00255497009837842!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00761101029727971!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0153882777688987!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108559003453531!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172662524141712!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663139199020659!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308589644804969!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328691803162744!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.013989632461646!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242435721014176!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388460393234881
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189688385077742!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279018670829452!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171494465521384!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00436462988571431!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321469684179145!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319904024249179!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461269534427377!ELK4#2005;3:16.235681658468:0.000233604395574599:0.00255497009837842!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00761101029727971!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0153882777688987!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108559003453531!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172662524141712!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663139199020659!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308589644804969!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328691803162744!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.013989632461646!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242435721014176!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388460393234881
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}}
}}

Revision as of 16:11, 26 November 2012


Full id: C3517_Wilms_small_left_Dendritic_brain_adrenal_Placental



Phase1 CAGE Peaks

Hg19::chr15:78423705..78423738,-p2@CIB2
Hg19::chr15:78423763..78423774,-p3@CIB2
Hg19::chr15:78423776..78423794,-p1@CIB2


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>

Cell Type
Ontology termp-valuen
ectodermal cell3.11e-0772
Uber Anatomy
Ontology termp-valuen
anatomical cluster9.07e-20373
ecto-epithelium3.59e-19104
neural plate6.18e-1982
presumptive neural plate6.18e-1982
ectoderm-derived structure2.61e-18171
ectoderm2.61e-18171
presumptive ectoderm2.61e-18171
central nervous system3.15e-1781
neurectoderm6.47e-1786
nervous system5.49e-1589
organ part1.04e-14218
multi-tissue structure5.97e-14342
cell layer6.12e-14309
epithelium9.46e-14306
neural tube1.59e-1356
neural rod1.59e-1356
future spinal cord1.59e-1356
neural keel1.59e-1356
pre-chordal neural plate2.85e-1361
brain1.14e-1268
future brain1.14e-1268
regional part of nervous system1.21e-1253
regional part of brain1.21e-1253
adult organism1.61e-12114
organ system subdivision2.02e-12223
structure with developmental contribution from neural crest2.15e-11132
renal system3.41e-1148
urinary system structure5.47e-1147
tube3.84e-10192
cavitated compound organ1.11e-0931
anatomical conduit1.97e-09240
regional part of forebrain7.81e-0941
forebrain7.81e-0941
anterior neural tube7.81e-0941
future forebrain7.81e-0941
compound organ1.19e-0868
kidney2.33e-0826
kidney mesenchyme2.33e-0826
upper urinary tract2.33e-0826
kidney rudiment2.33e-0826
kidney field2.33e-0826
brain grey matter3.57e-0834
gray matter3.57e-0834
cerebral hemisphere3.69e-0832
embryo6.73e-08592
telencephalon9.64e-0834
cerebral cortex1.06e-0725
pallium1.06e-0725
regional part of telencephalon1.42e-0732
multi-cellular organism2.89e-07656
anatomical system9.05e-07624
trunk region element9.61e-07101


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#90536.336201576962630.003930750035764890.0189688385077742
CTCF#1066435.360256373075030.0064925092527670.0279018670829452
CTCFL#140690319.74647435897440.0001298372005551160.00171494465521384
E2F4#1874312.66806031528440.0004917987006298980.00436462988571431
E2F6#187635.017155731697390.00791769806886330.0321469684179145
EGR1#195834.988179094810140.008056488137383440.0319904024249179
ELF1#199734.258097958807540.01295179875054610.0461269534427377
ELK4#2005316.2356816584680.0002336043955745990.00255497009837842
ETS1#211339.728760922202340.001085840092584840.00761101029727971
GABPB1#255337.067683836182170.002832212825417420.0153882777688987
HMGN3#932438.178547723350590.001827766942164210.0108559003453531
PAX5#507936.669565531177830.003370290999677260.0172662524141712
RAD21#5885310.35503389545630.0009004912073565420.00663139199020659
SMC3#9126315.04493284493280.0002935825420371870.00308589644804969
YY1#752834.911170749853860.008441455341808260.0328691803162744
ZBTB7A#5134137.35190930787590.002516255860282270.013989632461646
ZEB1#6935316.88843201754390.0002075486917327580.00242435721014176
ZNF143#7702313.50087655222790.0004062804962997170.00388460393234881



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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