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Coexpression cluster:C1045: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1045_Whole_blood_occipital_Neutrophils_cerebral_medial_hippocampus
|full_id=C1045_Whole_blood_occipital_Neutrophils_cerebral_medial_hippocampus
|gostat_on_coexpression_clusters=GO:0000151!ubiquitin 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 remodeling!0.0334074980632568!56172
|gostat_on_coexpression_clusters=GO:0000151!ubiquitin 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 remodeling!0.0334074980632568!56172

Revision as of 13:28, 12 September 2012


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 organism2.08e-46115
neural tube9.67e-2757
neural rod9.67e-2757
future spinal cord9.67e-2757
neural keel9.67e-2757
regional part of brain7.77e-2559
central nervous system2.06e-2382
brain7.89e-2369
future brain7.89e-2369
anterior neural tube2.55e-2142
neural plate3.16e-2186
presumptive neural plate3.16e-2186
regional part of forebrain5.09e-2141
forebrain5.09e-2141
future forebrain5.09e-2141
regional part of nervous system2.55e-2094
nervous system2.55e-2094
neurectoderm7.14e-1990
telencephalon3.04e-1734
gray matter3.26e-1734
brain grey matter3.26e-1734
ectoderm-derived structure3.51e-17169
multi-cellular organism4.31e-17659
head5.65e-17123
regional part of telencephalon1.34e-1633
cerebral hemisphere3.02e-1632
anterior region of body5.27e-16129
craniocervical region5.27e-16129
ectoderm8.10e-16173
presumptive ectoderm8.10e-16173
anatomical system1.39e-15625
anatomical group2.60e-15626
pre-chordal neural plate1.10e-1461
regional part of cerebral cortex1.41e-1422
anatomical conduit7.73e-14241
neocortex2.15e-1320
tube4.14e-13194
embryonic structure4.60e-13605
developing anatomical structure4.60e-13605
germ layer4.67e-13604
embryonic tissue4.67e-13604
presumptive structure4.67e-13604
epiblast (generic)4.67e-13604
cerebral cortex3.80e-1225
pallium3.80e-1225
embryo4.79e-12612
anatomical cluster3.50e-11286
organism subdivision6.81e-11365
epithelium4.62e-08309
organ5.38e-08511
cell layer8.67e-08312


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#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.