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Coexpression cluster:C3258: Difference between revisions

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|full_id=C3258_Neutrophils_Eosinophils_caudate_putamen_breast_oral_CD14
|full_id=C3258_Neutrophils_Eosinophils_caudate_putamen_breast_oral_CD14
|id=C3258
|id=C3258
|ontology_enrichment_celltype=CL:0000860!2.16e-16!45;CL:0002057!1.17e-15!42;CL:0000766!3.35e-09!76;CL:0002009!9.52e-07!65
|ontology_enrichment_celltype=CL:0000860!2.88e-16!42;CL:0002057!2.88e-16!42;CL:0000473!9.69e-11!48;CL:0000234!9.69e-11!48;CL:0000766!2.32e-08!72
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.05e-24!115;UBERON:0001049!2.01e-12!57;UBERON:0005068!2.01e-12!57;UBERON:0006241!2.01e-12!57;UBERON:0007135!2.01e-12!57;UBERON:0001017!5.02e-12!82;UBERON:0002780!9.88e-12!41;UBERON:0001890!9.88e-12!41;UBERON:0006240!9.88e-12!41;UBERON:0003080!1.11e-11!42;UBERON:0005743!1.57e-11!86;UBERON:0002616!2.58e-11!59;UBERON:0000955!2.96e-11!69;UBERON:0006238!2.96e-11!69;UBERON:0003075!3.54e-10!86;UBERON:0007284!3.54e-10!86;UBERON:0002346!7.20e-10!90;UBERON:0000468!2.59e-09!659;UBERON:0001893!2.69e-09!34;UBERON:0000073!2.85e-09!94;UBERON:0001016!2.85e-09!94;UBERON:0003056!2.90e-09!61;UBERON:0001869!3.35e-09!32;UBERON:0002020!4.44e-09!34;UBERON:0003528!4.44e-09!34;UBERON:0002791!5.04e-09!33;UBERON:0002619!7.76e-08!22;UBERON:0001950!2.69e-07!20;UBERON:0000062!2.77e-07!511;UBERON:0000153!6.47e-07!129;UBERON:0007811!6.47e-07!129
|ontology_enrichment_uberon=UBERON:0007023!1.97e-22!114;UBERON:0000073!1.61e-11!53;UBERON:0002616!1.61e-11!53;UBERON:0001017!4.03e-11!81;UBERON:0001049!5.27e-11!56;UBERON:0005068!5.27e-11!56;UBERON:0006241!5.27e-11!56;UBERON:0007135!5.27e-11!56;UBERON:0000955!2.85e-10!68;UBERON:0006238!2.85e-10!68;UBERON:0002780!3.51e-10!41;UBERON:0001890!3.51e-10!41;UBERON:0003080!3.51e-10!41;UBERON:0006240!3.51e-10!41;UBERON:0001016!8.80e-09!89;UBERON:0000468!2.68e-08!656;UBERON:0003075!3.46e-08!82;UBERON:0007284!3.46e-08!82;UBERON:0002346!5.80e-08!86;UBERON:0003528!6.40e-08!34;UBERON:0002020!6.40e-08!34;UBERON:0001893!7.41e-08!34;UBERON:0002791!7.75e-08!32;UBERON:0001869!9.11e-08!32;UBERON:0003056!2.05e-07!61;UBERON:0000062!8.22e-07!503
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189373375304571!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319394004168004!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127742734216966!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156297159607765!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00469853369421796!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275701244942748!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245662253244588!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00541053055608209!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00612160723321685!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139740107301935
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189373375304571!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319394004168004!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127742734216966!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156297159607765!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00469853369421796!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275701244942748!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245662253244588!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00541053055608209!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00612160723321685!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139740107301935
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}}
}}

Revision as of 14:56, 19 October 2012


Full id: C3258_Neutrophils_Eosinophils_caudate_putamen_breast_oral_CD14



Phase1 CAGE Peaks

Hg19::chr12:132379160..132379201,+p1@ULK1
Hg19::chr12:132379210..132379234,+p2@ULK1
Hg19::chr12:132379245..132379256,+p4@ULK1


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
classical monocyte2.88e-1642
CD14-positive, CD16-negative classical monocyte2.88e-1642
defensive cell9.69e-1148
phagocyte9.69e-1148
myeloid leukocyte2.32e-0872
Uber Anatomy
Ontology termp-valuen
adult organism1.97e-22114
regional part of nervous system1.61e-1153
regional part of brain1.61e-1153
central nervous system4.03e-1181
neural tube5.27e-1156
neural rod5.27e-1156
future spinal cord5.27e-1156
neural keel5.27e-1156
brain2.85e-1068
future brain2.85e-1068
regional part of forebrain3.51e-1041
forebrain3.51e-1041
anterior neural tube3.51e-1041
future forebrain3.51e-1041
nervous system8.80e-0989
multi-cellular organism2.68e-08656
neural plate3.46e-0882
presumptive neural plate3.46e-0882
neurectoderm5.80e-0886
brain grey matter6.40e-0834
gray matter6.40e-0834
telencephalon7.41e-0834
regional part of telencephalon7.75e-0832
cerebral hemisphere9.11e-0832
pre-chordal neural plate2.05e-0761
organ8.22e-07503


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#90536.336201576962630.003930750035764890.0189373375304571
EGR1#195834.988179094810140.008056488137383440.0319394004168004
IRF1#365937.63716375356390.002244692747297240.0127742734216966
JUND#372736.994663941871030.002921845042734990.0156297159607765
NRF1#4899312.21027944771090.0005492172401020010.00469853369421796
SIN3A#2594235.408884726815140.006318961977991520.0275701244942748
SP1#666735.69838137814090.005403962701712170.0245662253244588
TAF7#6879311.43306940492390.0006690181981945830.00541053055608209
TCF7L2#6934310.77017656313730.0008003181298398380.00612160723321685
ZBTB7A#5134137.35190930787590.002516255860282270.0139740107301935



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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