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Coexpression cluster:C1940: Difference between revisions

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|full_id=C1940_migratory_thalamus_cord_globus_substantia_hippocampus_CD14CD16
|full_id=C1940_migratory_thalamus_cord_globus_substantia_hippocampus_CD14CD16
|id=C1940
|id=C1940
|ontology_enrichment_celltype=CL:0000738!1.29e-40!140;CL:0002031!7.07e-35!124;CL:0002087!6.45e-34!119;CL:0000037!5.89e-32!172;CL:0000566!5.89e-32!172;CL:0000988!1.49e-29!182;CL:0002032!3.48e-29!165;CL:0000837!3.48e-29!165;CL:0000557!3.64e-21!71;CL:0000766!1.40e-20!76;CL:0000860!6.28e-20!45;CL:0002057!7.03e-20!42;CL:0000839!1.45e-19!70;CL:0002009!1.49e-19!65;CL:0002194!1.33e-18!63;CL:0000576!1.33e-18!63;CL:0000040!1.33e-18!63;CL:0000559!1.33e-18!63;CL:0000763!2.21e-15!112;CL:0000049!2.21e-15!112;CL:0000838!7.26e-14!52;CL:0000542!1.22e-13!53;CL:0000051!1.22e-13!53;CL:0000791!1.90e-08!18;CL:0000789!1.90e-08!18;CL:0002420!1.90e-08!18;CL:0002419!1.90e-08!18;CL:0000790!1.90e-08!18;CL:0000084!4.35e-08!25;CL:0000827!4.35e-08!25;CL:0000451!2.35e-07!10
|ontology_enrichment_celltype=CL:0000738!1.57e-46!136;CL:0002031!3.11e-40!120;CL:0002087!7.74e-40!115;CL:0000037!1.04e-33!168;CL:0000566!1.04e-33!168;CL:0000988!3.12e-33!177;CL:0002032!9.50e-31!161;CL:0000837!9.50e-31!161;CL:0000557!7.77e-27!67;CL:0002009!5.30e-26!61;CL:0000860!1.90e-25!42;CL:0002057!1.90e-25!42;CL:0000766!4.30e-25!72;CL:0000839!7.01e-25!66;CL:0000473!7.22e-25!48;CL:0000234!7.22e-25!48;CL:0002194!9.11e-25!59;CL:0000576!9.11e-25!59;CL:0000040!9.11e-25!59;CL:0000559!9.11e-25!59;CL:0000763!4.81e-17!108;CL:0000049!4.81e-17!108;CL:0000838!9.85e-14!52;CL:0000542!3.31e-13!53;CL:0000051!3.31e-13!53;CL:0002242!3.21e-12!55;CL:0000084!5.39e-10!25;CL:0000827!5.39e-10!25;CL:0000791!5.61e-10!18;CL:0000789!5.61e-10!18;CL:0002420!5.61e-10!18;CL:0002419!5.61e-10!18;CL:0000790!5.61e-10!18;CL:0000451!5.71e-09!10;CL:0000990!1.20e-07!8;CL:0002393!1.96e-07!9;CL:0002397!1.96e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.22e-37!115;UBERON:0001049!7.90e-26!57;UBERON:0005068!7.90e-26!57;UBERON:0006241!7.90e-26!57;UBERON:0007135!7.90e-26!57;UBERON:0002390!7.96e-26!102;UBERON:0003061!7.96e-26!102;UBERON:0002193!6.19e-21!112;UBERON:0002780!8.44e-21!41;UBERON:0001890!8.44e-21!41;UBERON:0006240!8.44e-21!41;UBERON:0003080!9.11e-21!42;UBERON:0002616!3.05e-20!59;UBERON:0005743!1.44e-18!86;UBERON:0001017!1.53e-18!82;UBERON:0001893!5.26e-18!34;UBERON:0002020!6.64e-18!34;UBERON:0003528!6.64e-18!34;UBERON:0002791!1.99e-17!33;UBERON:0000955!2.26e-17!69;UBERON:0006238!2.26e-17!69;UBERON:0003075!2.27e-17!86;UBERON:0007284!2.27e-17!86;UBERON:0002371!3.28e-17!80;UBERON:0001869!1.23e-16!32;UBERON:0000073!2.40e-15!94;UBERON:0001016!2.40e-15!94;UBERON:0002346!2.60e-15!90;UBERON:0001474!6.76e-15!86;UBERON:0003056!8.85e-13!61;UBERON:0002619!2.82e-12!22;UBERON:0002405!2.96e-12!115;UBERON:0000956!2.96e-12!25;UBERON:0000203!2.96e-12!25;UBERON:0001950!3.23e-11!20;UBERON:0004765!1.60e-10!101;UBERON:0001434!1.60e-10!101;UBERON:0000153!1.05e-08!129;UBERON:0007811!1.05e-08!129;UBERON:0000033!2.66e-07!123;UBERON:0002308!2.73e-07!9;UBERON:0000125!2.73e-07!9;UBERON:0000178!4.48e-07!15;UBERON:0000179!4.48e-07!15;UBERON:0000463!4.48e-07!15;UBERON:0002420!5.50e-07!9;UBERON:0007245!5.50e-07!9;UBERON:0010009!5.50e-07!9;UBERON:0010011!5.50e-07!9;UBERON:0000454!5.50e-07!9
|ontology_enrichment_uberon=UBERON:0002390!5.37e-32!98;UBERON:0003061!5.37e-32!98;UBERON:0007023!1.09e-31!114;UBERON:0001049!4.06e-28!56;UBERON:0005068!4.06e-28!56;UBERON:0006241!4.06e-28!56;UBERON:0007135!4.06e-28!56;UBERON:0002193!6.87e-28!108;UBERON:0000073!7.41e-26!53;UBERON:0002616!7.41e-26!53;UBERON:0002780!2.12e-22!41;UBERON:0001890!2.12e-22!41;UBERON:0003080!2.12e-22!41;UBERON:0006240!2.12e-22!41;UBERON:0002371!7.11e-22!76;UBERON:0002405!1.14e-21!93;UBERON:0001474!6.13e-20!82;UBERON:0001893!1.73e-18!34;UBERON:0003528!2.41e-18!34;UBERON:0002020!2.41e-18!34;UBERON:0001017!6.04e-18!81;UBERON:0000955!1.69e-17!68;UBERON:0006238!1.69e-17!68;UBERON:0002791!5.94e-17!32;UBERON:0004765!7.87e-17!90;UBERON:0001869!7.92e-17!32;UBERON:0003075!1.26e-15!82;UBERON:0007284!1.26e-15!82;UBERON:0001016!5.01e-15!89;UBERON:0001434!1.50e-14!100;UBERON:0002346!5.27e-14!86;UBERON:0003056!2.43e-12!61;UBERON:0002619!9.74e-12!22;UBERON:0000956!2.65e-11!25;UBERON:0000203!2.65e-11!25;UBERON:0001950!2.90e-10!20;UBERON:0010371!1.62e-09!104;UBERON:0000125!3.91e-09!9;UBERON:0002308!3.91e-09!9;UBERON:0009663!9.49e-08!7;UBERON:0000178!2.14e-07!15;UBERON:0000179!2.14e-07!15;UBERON:0000463!2.14e-07!15;UBERON:0002420!2.28e-07!9;UBERON:0007245!2.28e-07!9;UBERON:0010009!2.28e-07!9;UBERON:0010011!2.28e-07!9;UBERON:0000454!2.28e-07!9;UBERON:0003076!5.59e-07!15;UBERON:0003057!5.59e-07!15
|tf_chipseq_enrich=E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00353444325113916!EBF1#1879;3:5.3438801079414:0.0118761556386811:0.0432458358756048!GATA3#2625;2:10.8946065428824:0.012515829121883:0.0452861931007602!MAFK#7975;3:16.2604398826979:0.000474821142383054:0.00435801435006097!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135527902720644
|tf_chipseq_enrich=E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00353444325113916!EBF1#1879;3:5.3438801079414:0.0118761556386811:0.0432458358756048!GATA3#2625;2:10.8946065428824:0.012515829121883:0.0452861931007602!MAFK#7975;3:16.2604398826979:0.000474821142383054:0.00435801435006097!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135527902720644
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}}
}}

Revision as of 11:52, 19 October 2012


Full id: C1940_migratory_thalamus_cord_globus_substantia_hippocampus_CD14CD16



Phase1 CAGE Peaks

Hg19::chr4:36245643..36245697,-p5@ARAP2
Hg19::chr4:36245700..36245716,-p13@ARAP2
Hg19::chr4:36246367..36246380,-p12@ARAP2
Hg19::chr4:36246391..36246453,-p2@ARAP2
Hg19::chr4:36246458..36246477,-p8@ARAP2


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
leukocyte1.57e-46136
hematopoietic lineage restricted progenitor cell3.11e-40120
nongranular leukocyte7.74e-40115
hematopoietic stem cell1.04e-33168
angioblastic mesenchymal cell1.04e-33168
hematopoietic cell3.12e-33177
hematopoietic oligopotent progenitor cell9.50e-31161
hematopoietic multipotent progenitor cell9.50e-31161
granulocyte monocyte progenitor cell7.77e-2767
macrophage dendritic cell progenitor5.30e-2661
classical monocyte1.90e-2542
CD14-positive, CD16-negative classical monocyte1.90e-2542
myeloid leukocyte4.30e-2572
myeloid lineage restricted progenitor cell7.01e-2566
defensive cell7.22e-2548
phagocyte7.22e-2548
monopoietic cell9.11e-2559
monocyte9.11e-2559
monoblast9.11e-2559
promonocyte9.11e-2559
myeloid cell4.81e-17108
common myeloid progenitor4.81e-17108
lymphoid lineage restricted progenitor cell9.85e-1452
lymphocyte3.31e-1353
common lymphoid progenitor3.31e-1353
nucleate cell3.21e-1255
T cell5.39e-1025
pro-T cell5.39e-1025
mature alpha-beta T cell5.61e-1018
alpha-beta T cell5.61e-1018
immature T cell5.61e-1018
mature T cell5.61e-1018
immature alpha-beta T cell5.61e-1018
dendritic cell5.71e-0910
conventional dendritic cell1.20e-078
intermediate monocyte1.96e-079
CD14-positive, CD16-positive monocyte1.96e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.37e-3298
blood island5.37e-3298
adult organism1.09e-31114
neural tube4.06e-2856
neural rod4.06e-2856
future spinal cord4.06e-2856
neural keel4.06e-2856
hemolymphoid system6.87e-28108
regional part of nervous system7.41e-2653
regional part of brain7.41e-2653
regional part of forebrain2.12e-2241
forebrain2.12e-2241
anterior neural tube2.12e-2241
future forebrain2.12e-2241
bone marrow7.11e-2276
immune system1.14e-2193
bone element6.13e-2082
telencephalon1.73e-1834
brain grey matter2.41e-1834
gray matter2.41e-1834
central nervous system6.04e-1881
brain1.69e-1768
future brain1.69e-1768
regional part of telencephalon5.94e-1732
skeletal element7.87e-1790
cerebral hemisphere7.92e-1732
neural plate1.26e-1582
presumptive neural plate1.26e-1582
nervous system5.01e-1589
skeletal system1.50e-14100
neurectoderm5.27e-1486
pre-chordal neural plate2.43e-1261
regional part of cerebral cortex9.74e-1222
cerebral cortex2.65e-1125
pallium2.65e-1125
neocortex2.90e-1020
ecto-epithelium1.62e-09104
neural nucleus3.91e-099
nucleus of brain3.91e-099
telencephalic nucleus9.49e-087
blood2.14e-0715
haemolymphatic fluid2.14e-0715
organism substance2.14e-0715
basal ganglion2.28e-079
nuclear complex of neuraxis2.28e-079
aggregate regional part of brain2.28e-079
collection of basal ganglia2.28e-079
cerebral subcortex2.28e-079
posterior neural tube5.59e-0715
chordal neural plate5.59e-0715


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
E2F1#186954.907389214879320.0003512818099256460.00353444325113916
EBF1#187935.34388010794140.01187615563868110.0432458358756048
GATA3#2625210.89460654288240.0125158291218830.0452861931007602
MAFK#7975316.26043988269790.0004748211423830540.00435801435006097
TAF1#687253.343046285745290.002394600090870310.0135527902720644



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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