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Difference between revisions of "Coexpression cluster:C1130"

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|ontology_enrichment_celltype=
 
|ontology_enrichment_celltype=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.07e-44!115;UBERON:0001049!1.36e-25!57;UBERON:0005068!1.36e-25!57;UBERON:0006241!1.36e-25!57;UBERON:0007135!1.36e-25!57;UBERON:0002616!1.11e-23!59;UBERON:0003080!3.21e-22!42;UBERON:0002780!9.41e-22!41;UBERON:0001890!9.41e-22!41;UBERON:0006240!9.41e-22!41;UBERON:0000955!3.26e-21!69;UBERON:0006238!3.26e-21!69;UBERON:0001017!1.21e-18!82;UBERON:0003075!4.67e-18!86;UBERON:0007284!4.67e-18!86;UBERON:0005743!4.78e-18!86;UBERON:0001893!9.33e-18!34;UBERON:0002020!9.44e-18!34;UBERON:0003528!9.44e-18!34;UBERON:0002346!1.52e-17!90;UBERON:0000073!2.99e-17!94;UBERON:0001016!2.99e-17!94;UBERON:0002791!4.01e-17!33;UBERON:0001869!1.86e-16!32;UBERON:0000153!4.08e-16!129;UBERON:0007811!4.08e-16!129;UBERON:0000033!5.08e-16!123;UBERON:0002619!8.49e-14!22;UBERON:0001950!1.38e-12!20;UBERON:0004121!2.23e-12!169;UBERON:0000924!2.86e-12!173;UBERON:0006601!2.86e-12!173;UBERON:0000956!3.96e-12!25;UBERON:0000203!3.96e-12!25;UBERON:0003056!1.06e-11!61;UBERON:0004111!5.26e-10!241;UBERON:0000477!1.17e-09!286;UBERON:0000475!3.11e-09!365;UBERON:0000025!6.60e-08!194;UBERON:0002308!2.86e-07!9;UBERON:0000125!2.86e-07!9;UBERON:0002420!3.48e-07!9;UBERON:0007245!3.48e-07!9;UBERON:0010009!3.48e-07!9;UBERON:0010011!3.48e-07!9;UBERON:0000454!3.48e-07!9
+
|ontology_enrichment_uberon=UBERON:0007023!2.17e-44!114;UBERON:0001049!2.75e-25!56;UBERON:0005068!2.75e-25!56;UBERON:0006241!2.75e-25!56;UBERON:0007135!2.75e-25!56;UBERON:0000073!1.66e-23!53;UBERON:0002616!1.66e-23!53;UBERON:0000955!6.97e-22!68;UBERON:0006238!6.97e-22!68;UBERON:0002780!1.79e-21!41;UBERON:0001890!1.79e-21!41;UBERON:0003080!1.79e-21!41;UBERON:0006240!1.79e-21!41;UBERON:0001017!9.34e-20!81;UBERON:0001016!5.83e-19!89;UBERON:0003528!1.51e-17!34;UBERON:0002020!1.51e-17!34;UBERON:0001893!1.52e-17!34;UBERON:0003075!5.89e-17!82;UBERON:0007284!5.89e-17!82;UBERON:0002346!7.99e-17!86;UBERON:0010314!2.35e-16!132;UBERON:0001869!2.57e-16!32;UBERON:0002791!2.67e-16!32;UBERON:0002619!2.33e-14!22;UBERON:0001950!4.04e-13!20;UBERON:0004121!4.89e-12!171;UBERON:0000924!4.89e-12!171;UBERON:0006601!4.89e-12!171;UBERON:0000956!5.74e-12!25;UBERON:0000203!5.74e-12!25;UBERON:0003056!5.87e-12!61;UBERON:0011216!1.96e-10!223;UBERON:0010371!3.00e-10!104;UBERON:0004111!2.41e-08!240;UBERON:0000481!7.20e-08!342;UBERON:0000477!1.26e-07!373;UBERON:0000125!3.12e-07!9;UBERON:0002308!3.12e-07!9;UBERON:0002420!3.22e-07!9;UBERON:0007245!3.22e-07!9;UBERON:0010009!3.22e-07!9;UBERON:0010011!3.22e-07!9;UBERON:0000454!3.22e-07!9
 
|tf_chipseq_enrich=EGR1#1958;5:3.56298506772153:0.00472235121105893:0.0222572154940107!ELF1#1997;6:3.64979825040646:0.000937747978262069:0.0067884841686915!HEY1#23462;6:3.46295232266204:0.00126789009587212:0.00850408925070894!HMGN3#9324;4:4.67345584191462:0.00575188109993887:0.0259054168009192!MYC#4609;5:3.73020133686386:0.00382194422230669:0.0188674623101479!NR2C2#7182;3:13.9776903879604:0.00091899130724013:0.00668234582864666!PAX5#5079;4:3.81118030353019:0.0120826168155519:0.0438234560722147!POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223250068866263!TAF1#6872;6:2.86546824492454:0.00372833020747146:0.0185827564445028
 
|tf_chipseq_enrich=EGR1#1958;5:3.56298506772153:0.00472235121105893:0.0222572154940107!ELF1#1997;6:3.64979825040646:0.000937747978262069:0.0067884841686915!HEY1#23462;6:3.46295232266204:0.00126789009587212:0.00850408925070894!HMGN3#9324;4:4.67345584191462:0.00575188109993887:0.0259054168009192!MYC#4609;5:3.73020133686386:0.00382194422230669:0.0188674623101479!NR2C2#7182;3:13.9776903879604:0.00091899130724013:0.00668234582864666!PAX5#5079;4:3.81118030353019:0.0120826168155519:0.0438234560722147!POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223250068866263!TAF1#6872;6:2.86546824492454:0.00372833020747146:0.0185827564445028
 
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}}
 
}}

Revision as of 01:53, 19 October 2012


Full id: C1130_optic_globus_thalamus_spinal_occipital_locus_pons



Phase1 CAGE Peaks

  Short description
Hg19::chr11:111848024..111848087,+ p1@DIXDC1
Hg19::chr1:78245303..78245351,+ p1@FAM73A
Hg19::chr20:16554078..16554113,- p2@KIF16B
Hg19::chr2:73053126..73053184,- p1@EXOC6B
Hg19::chr5:139487363..139487444,+ p1@PURA
Hg19::chr5:139487608..139487663,+ p3@PURA
Hg19::chr6:126112074..126112144,+ p1@NCOA7


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0003691double-stranded telomeric DNA binding0.0250906422742618
GO:0005662DNA replication factor A complex0.0250906422742618
GO:0000784nuclear chromosome, telomeric region0.0250906422742618
GO:0043601nuclear replisome0.0250906422742618
GO:0030894replisome0.0250906422742618
GO:0000145exocyst0.0250906422742618
GO:0042162telomeric DNA binding0.0250906422742618
GO:0046332SMAD binding0.0250906422742618
GO:0006268DNA unwinding during replication0.0250906422742618
GO:0043596nuclear replication fork0.0250906422742618
GO:0032392DNA geometric change0.0250906422742618
GO:0032508DNA duplex unwinding0.0250906422742618
GO:0016998cell wall catabolic process0.0250906422742618
GO:0010382cell wall metabolic process0.0250906422742618
GO:0007047cell wall organization and biogenesis0.0250906422742618
GO:0045229external encapsulating structure organization and biogenesis0.025871678251679
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0298750678121566
GO:0000781chromosome, telomeric region0.0310576474269521
GO:0005657replication fork0.0310576474269521
GO:0006904vesicle docking during exocytosis0.0310576474269521
GO:0006270DNA replication initiation0.0310576474269521
GO:0048278vesicle docking0.0310576474269521
GO:0022406membrane docking0.0310576474269521
GO:0044448cell cortex part0.0352318202835125
GO:0003697single-stranded DNA binding0.0458051730286997
GO:0005938cell cortex0.0462013451222497
GO:0044454nuclear chromosome part0.0465674358244908



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset


uberon_data


Uber Anatomy
Ontology termp-valuen
adult organism2.17e-44114
neural tube2.75e-2556
neural rod2.75e-2556
future spinal cord2.75e-2556
neural keel2.75e-2556
regional part of nervous system1.66e-2353
regional part of brain1.66e-2353
brain6.97e-2268
future brain6.97e-2268
regional part of forebrain1.79e-2141
forebrain1.79e-2141
anterior neural tube1.79e-2141
future forebrain1.79e-2141
central nervous system9.34e-2081
nervous system5.83e-1989
brain grey matter1.51e-1734
gray matter1.51e-1734
telencephalon1.52e-1734
neural plate5.89e-1782
presumptive neural plate5.89e-1782
neurectoderm7.99e-1786
structure with developmental contribution from neural crest2.35e-16132
cerebral hemisphere2.57e-1632
regional part of telencephalon2.67e-1632
regional part of cerebral cortex2.33e-1422
neocortex4.04e-1320
ectoderm-derived structure4.89e-12171
ectoderm4.89e-12171
presumptive ectoderm4.89e-12171
cerebral cortex5.74e-1225
pallium5.74e-1225
pre-chordal neural plate5.87e-1261
organ system subdivision1.96e-10223
ecto-epithelium3.00e-10104
anatomical conduit2.41e-08240
multi-tissue structure7.20e-08342
anatomical cluster1.26e-07373
neural nucleus3.12e-079
nucleus of brain3.12e-079
basal ganglion3.22e-079
nuclear complex of neuraxis3.22e-079
aggregate regional part of brain3.22e-079
collection of basal ganglia3.22e-079
cerebral subcortex3.22e-079


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
EGR1#195853.562985067721530.004722351211058930.0222572154940107
ELF1#199763.649798250406460.0009377479782620690.0067884841686915
HEY1#2346263.462952322662040.001267890095872120.00850408925070894
HMGN3#932444.673455841914620.005751881099938870.0259054168009192
MYC#460953.730201336863860.003821944222306690.0188674623101479
NR2C2#7182313.97769038796040.000918991307240130.00668234582864666
PAX5#507943.811180303530190.01208261681555190.0438234560722147
POLR2A#543072.147453176558070.004747636447610280.0223250068866263
TAF1#687262.865468244924540.003728330207471460.0185827564445028



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.