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Coexpression cluster:C1843: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.40e-25!115;UBERON:0001049!1.29e-20!57;UBERON:0005068!1.29e-20!57;UBERON:0006241!1.29e-20!57;UBERON:0007135!1.29e-20!57;UBERON:0002616!1.54e-18!59;UBERON:0005743!1.64e-18!86;UBERON:0000073!2.78e-18!94;UBERON:0001016!2.78e-18!94;UBERON:0001017!4.78e-17!82;UBERON:0002780!1.59e-16!41;UBERON:0001890!1.59e-16!41;UBERON:0006240!1.59e-16!41;UBERON:0000955!4.05e-16!69;UBERON:0006238!4.05e-16!69;UBERON:0003080!7.21e-16!42;UBERON:0003075!3.08e-15!86;UBERON:0007284!3.08e-15!86;UBERON:0002346!7.83e-15!90;UBERON:0001893!3.49e-12!34;UBERON:0003056!1.05e-11!61;UBERON:0002020!1.46e-11!34;UBERON:0003528!1.46e-11!34;UBERON:0002791!1.67e-11!33;UBERON:0000153!6.35e-11!129;UBERON:0007811!6.35e-11!129;UBERON:0001869!6.85e-11!32;UBERON:0001950!6.85e-10!20;UBERON:0000033!1.68e-09!123;UBERON:0002619!1.76e-09!22;UBERON:0000956!9.71e-08!25;UBERON:0000203!9.71e-08!25;UBERON:0004121!1.47e-07!169;UBERON:0000924!1.61e-07!173;UBERON:0006601!1.61e-07!173
|ontology_enrichment_uberon=UBERON:0007023!3.40e-25!115;UBERON:0001049!1.29e-20!57;UBERON:0005068!1.29e-20!57;UBERON:0006241!1.29e-20!57;UBERON:0007135!1.29e-20!57;UBERON:0002616!1.54e-18!59;UBERON:0005743!1.64e-18!86;UBERON:0000073!2.78e-18!94;UBERON:0001016!2.78e-18!94;UBERON:0001017!4.78e-17!82;UBERON:0002780!1.59e-16!41;UBERON:0001890!1.59e-16!41;UBERON:0006240!1.59e-16!41;UBERON:0000955!4.05e-16!69;UBERON:0006238!4.05e-16!69;UBERON:0003080!7.21e-16!42;UBERON:0003075!3.08e-15!86;UBERON:0007284!3.08e-15!86;UBERON:0002346!7.83e-15!90;UBERON:0001893!3.49e-12!34;UBERON:0003056!1.05e-11!61;UBERON:0002020!1.46e-11!34;UBERON:0003528!1.46e-11!34;UBERON:0002791!1.67e-11!33;UBERON:0000153!6.35e-11!129;UBERON:0007811!6.35e-11!129;UBERON:0001869!6.85e-11!32;UBERON:0001950!6.85e-10!20;UBERON:0000033!1.68e-09!123;UBERON:0002619!1.76e-09!22;UBERON:0000956!9.71e-08!25;UBERON:0000203!9.71e-08!25;UBERON:0004121!1.47e-07!169;UBERON:0000924!1.61e-07!173;UBERON:0006601!1.61e-07!173
|tf_chipseq_enrich=BATF#10538;4:19.4862414338429:1.37275300118359e-05:0.000332257127904086!CEBPB#1051;4:6.37691810065985:0.00111394417667732:0.00765540671632573!EBF1#1879;4:7.1251734772552:0.000723053104677421:0.00577198984937745!EP300#2033;4:5.41915338097856:0.0020938692794389:0.0121186818329354!FOXA1#3169;4:8.86513579950836:0.000307546859137271:0.00316764165891888!GATA3#2625;4:21.7892130857648:8.81158303710445e-06:0.000237612424686845!HDAC2#3066;4:10.732496189301:0.000145096579747875:0.00188620135577399!NFKB1#4790;4:4.39045073935507:0.00470773269252496:0.022206354486004!SMARCC2#6601;4:75.3242995415181:6.28893529700036e-08:3.88415206081266e-06!SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00714296307302439!STAT1#6772;4:16.5652699977594:2.61308619905866e-05:0.000564092826671118
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}}
}}

Revision as of 11:34, 5 September 2012


Full id: C1843_signet_lung_cord_bile_colon_retina_adenocarcinoma



Phase1 CAGE Peaks

Hg19::chr1:205905161..205905166,-p5@SLC26A9
Hg19::chr7:129008057..129008070,+p10@AHCYL2
Hg19::chr7:129008104..129008114,+p15@AHCYL2
Hg19::chr7:129008147..129008158,+p7@AHCYL2
Hg19::chr7:129008160..129008180,+p5@AHCYL2


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:0015116sulfate transmembrane transporter activity0.00582832921229247
GO:0008271secondary active sulfate transmembrane transporter activity0.00582832921229247
GO:0008272sulfate transport0.00582832921229247
GO:0015103inorganic anion transmembrane transporter activity0.0114947603909102
GO:0008509anion transmembrane transporter activity0.027069351230425
GO:0015698inorganic anion transport0.0280623258369638
GO:0006820anion transport0.0291416460614624
GO:0015291secondary active transmembrane transporter activity0.0291416460614624
GO:0022804active transmembrane transporter activity0.0481376820126379



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
classical monocyte7.02e-0745
Uber Anatomy
Ontology termp-valuen
adult organism3.40e-25115
neural tube1.29e-2057
neural rod1.29e-2057
future spinal cord1.29e-2057
neural keel1.29e-2057
regional part of brain1.54e-1859
regional part of nervous system2.78e-1894
nervous system2.78e-1894
central nervous system4.78e-1782
regional part of forebrain1.59e-1641
forebrain1.59e-1641
future forebrain1.59e-1641
brain4.05e-1669
future brain4.05e-1669
anterior neural tube7.21e-1642
neural plate3.08e-1586
presumptive neural plate3.08e-1586
neurectoderm7.83e-1590
telencephalon3.49e-1234
pre-chordal neural plate1.05e-1161
gray matter1.46e-1134
brain grey matter1.46e-1134
regional part of telencephalon1.67e-1133
anterior region of body6.35e-11129
craniocervical region6.35e-11129
cerebral hemisphere6.85e-1132
neocortex6.85e-1020
head1.68e-09123
regional part of cerebral cortex1.76e-0922
cerebral cortex9.71e-0825
pallium9.71e-0825
ectoderm-derived structure1.47e-07169
ectoderm1.61e-07173
presumptive ectoderm1.61e-07173


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
BATF#10538419.48624143384291.37275300118359e-050.000332257127904086
CEBPB#105146.376918100659850.001113944176677320.00765540671632573
EBF1#187947.12517347725520.0007230531046774210.00577198984937745
EP300#203345.419153380978560.00209386927943890.0121186818329354
FOXA1#316948.865135799508360.0003075468591372710.00316764165891888
GATA3#2625421.78921308576488.81158303710445e-060.000237612424686845
HDAC2#3066410.7324961893010.0001450965797478750.00188620135577399
NFKB1#479044.390450739355070.004707732692524960.022206354486004
SMARCC2#6601475.32429954151816.28893529700036e-083.88415206081266e-06
SPI1#668846.563458806818180.0009957429636454020.00714296307302439
STAT1#6772416.56526999775942.61308619905866e-050.000564092826671118



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.