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Coexpression cluster:C1045: Difference between revisions

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{{Coexpression_clusters
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ligase complex!0.00662310137760508!26994;10444$GO:0005517!calmodulin inhibitor activity!0.00662310137760508!5534$GO:0031462!Cul2-RING ubiquitin ligase complex!0.00662310137760508!10444$GO:0030504!inorganic diphosphate transmembrane transporter activity!0.00662310137760508!56172$GO:0004723!calcium-dependent protein serine/threonine phosphatase activity!0.0105961823506016!5534$GO:0051438!regulation of ubiquitin-protein ligase activity!0.0132432785339017!10444$GO:0005315!inorganic phosphate transmembrane transporter activity!0.0132432785339017!56172$GO:0005955!calcineurin complex!0.0132432785339017!5534$GO:0042787!protein ubiquitination during ubiquitin-dependent protein catabolic process!0.0144450866570246!26994$GO:0051340!regulation of ligase activity!0.0144450866570246!10444$GO:0050811!GABA receptor binding!0.0144450866570246!11345$GO:0048487!beta-tubulin binding!0.022062386928359!11345$GO:0030500!regulation of bone mineralization!0.0224001597406885!56172$GO:0015114!phosphate transmembrane transporter activity!0.0264670722043128!56172$GO:0030278!regulation of ossification!0.0311239866203646!56172$GO:0031461!cullin-RING ubiquitin ligase complex!0.0311239866203646!10444$GO:0030282!bone mineralization!0.0311239866203646!56172$GO:0006512!ubiquitin cycle!0.031212021879642!26994;10444$GO:0046850!regulation of bone 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|full_id=C1045_Whole_blood_occipital_Neutrophils_cerebral_medial_hippocampus
|id=C1045
}}

Latest revision as of 11:36, 17 September 2013


Full id: C1045_Whole_blood_occipital_Neutrophils_cerebral_medial_hippocampus



Phase1 CAGE Peaks

Hg19::chr16:75600247..75600325,+p1@GABARAPL2
Hg19::chr1:51701924..51702001,+p1@RNF11
Hg19::chr1:51702002..51702030,+p2@RNF11
Hg19::chr1:51702031..51702042,+p4@RNF11
Hg19::chr2:68479614..68479685,-p1@PPP3R1
Hg19::chr5:14872052..14872082,-p5@ANKH
Hg19::chr6:44095263..44095325,+p1@TMEM63B
Hg19::chr9:131534188..131534227,-p1@ZER1


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:0000151ubiquitin ligase complex0.00662310137760508
GO:0005517calmodulin inhibitor activity0.00662310137760508
GO:0031462Cul2-RING ubiquitin ligase complex0.00662310137760508
GO:0030504inorganic diphosphate transmembrane transporter activity0.00662310137760508
GO:0004723calcium-dependent protein serine/threonine phosphatase activity0.0105961823506016
GO:0051438regulation of ubiquitin-protein ligase activity0.0132432785339017
GO:0005315inorganic phosphate transmembrane transporter activity0.0132432785339017
GO:0005955calcineurin complex0.0132432785339017
GO:0042787protein ubiquitination during ubiquitin-dependent protein catabolic process0.0144450866570246
GO:0051340regulation of ligase activity0.0144450866570246
GO:0050811GABA receptor binding0.0144450866570246
GO:0048487beta-tubulin binding0.022062386928359
GO:0030500regulation of bone mineralization0.0224001597406885
GO:0015114phosphate transmembrane transporter activity0.0264670722043128
GO:0030278regulation of ossification0.0311239866203646
GO:0031461cullin-RING ubiquitin ligase complex0.0311239866203646
GO:0030282bone mineralization0.0311239866203646
GO:0006512ubiquitin cycle0.031212021879642
GO:0046850regulation of bone remodeling0.0334074980632568



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
adult organism3.03e-45114
neural tube4.12e-2656
neural rod4.12e-2656
future spinal cord4.12e-2656
neural keel4.12e-2656
regional part of nervous system1.26e-2453
regional part of brain1.26e-2453
brain3.98e-2268
future brain3.98e-2268
central nervous system4.09e-2281
regional part of forebrain1.13e-2041
forebrain1.13e-2041
anterior neural tube1.13e-2041
future forebrain1.13e-2041
neural plate3.33e-2082
presumptive neural plate3.33e-2082
nervous system3.72e-2089
neurectoderm7.77e-1886
multi-cellular organism3.50e-17656
telencephalon5.07e-1734
brain grey matter5.31e-1734
gray matter5.31e-1734
ecto-epithelium2.08e-16104
cerebral hemisphere4.83e-1632
regional part of telencephalon6.96e-1632
structure with developmental contribution from neural crest1.03e-15132
anatomical system2.30e-15624
anatomical group4.15e-15625
pre-chordal neural plate1.11e-1461
ectoderm-derived structure1.92e-14171
ectoderm1.92e-14171
presumptive ectoderm1.92e-14171
regional part of cerebral cortex2.53e-1422
embryonic structure4.60e-14564
germ layer6.60e-14560
germ layer / neural crest6.60e-14560
embryonic tissue6.60e-14560
presumptive structure6.60e-14560
germ layer / neural crest derived structure6.60e-14560
epiblast (generic)6.60e-14560
neocortex3.64e-1320
developing anatomical structure7.30e-13581
embryo3.31e-12592
cerebral cortex5.19e-1225
pallium5.19e-1225
anatomical conduit4.63e-11240
tube7.39e-11192
organ1.48e-08503
anatomical cluster8.22e-08373
organ system subdivision2.00e-07223


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)
MA0003.16.33181
MA0004.10.455723
MA0006.11.47431
MA0007.10.437331
MA0009.10.918715
MA0014.13.20776
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.11.52958
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.15.09623
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.18.18582
MA0056.10
MA0057.12.14064
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.961853
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.11.33409
MA0069.10.903908
MA0070.10.892666
MA0071.11.28975
MA0072.10.888148
MA0073.13.70374
MA0074.10.552456
MA0076.11.74818
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.770971
MA0089.10
MA0090.10.391903
MA0091.12.02209
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.11.49614
MA0103.10.291333
MA0105.10.988431
MA0106.10.59853
MA0107.10.666147
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.11.94086
MA0117.10.956472
MA0119.10.913661
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.916926
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.830366
MA0146.11.26525
MA0147.10.681318
MA0148.10.480298
MA0149.10.506665
MA0062.21.50503
MA0035.20.515566
MA0039.23.94096
MA0138.22.6595
MA0002.20.179788
MA0137.20.321796
MA0104.20.55506
MA0047.20.586412
MA0112.20.458158
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.577214
MA0155.11.64163
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.11.26616
MA0160.10.495355
MA0161.10
MA0162.15.01481
MA0163.11.42814
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.219.0644
MA0102.21.46209
MA0258.10.209744
MA0259.10.699589
MA0442.10



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#90586.336201576962633.84606837428661e-071.87525459823585e-05
E2F1#186974.293965563019419.58670853279727e-050.0013704164419064
E2F6#187674.390011265235218.25033297218753e-050.00124015043938154
EGR1#195874.364656707958878.58120841941444e-050.00128618373437891
ELF1#199784.258097958807549.24826870984006e-060.000246460815459808
ETS1#211344.864380461101170.0055537915159820.0251368334620864
FOSL2#235536.348825226710630.009211946658641070.034825399879889
GABPB1#255376.18422335665947.95182205325426e-060.000221166536197023
HDAC2#306646.707810118313130.001690987380029690.0105662935851933
HEY1#2346273.53509716271750.0003566123056684080.0035677969720953
HMGN3#932477.156229257931772.91658210831366e-060.000100034456095294
IRF1#365976.682518284368414.6709523292352e-060.000145101008421474
MAX#414954.032847193129450.003311981318472050.0171313960140608
MYC#460963.916711403707050.0009649270569246440.00693954117188768
NFKB1#479064.116047568145380.0007299856589784310.00581577330368818
PAX5#507954.168478456986140.002847508706107280.0154368524140742
POLR2A#543082.147453176558070.002210725788971910.0127195896140611
REST#597844.825014358064010.005720735398269540.0257862703608059
SIN3A#2594274.732774135963244.948745034002e-050.000847977001814823
SP1#666764.273786033605670.0005904726864288940.00494375315840526
TAF1#687272.925165500027130.001265325357915740.00849124944132635
TBP#690873.243424351209340.0006354223620492050.00521269940067999
TCF12#693856.646540563866510.0003223768920812840.00329988437048684
TRIM28#1015536.971446891973450.007100847201045050.0296061871064691
YY1#752874.297274406122129.53674534900876e-050.00136439472260976
ZBTB7A#5134187.35190930787591.17052559937328e-076.76153335580455e-06
ZEB1#6935510.55527001096493.50000145603859e-050.000682098623002826



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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