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Difference between revisions of "Coexpression cluster:C3251"

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|full_id=C3251_granulocyte_Burkitt_acute_signet_diffuse_splenic_biphenotypic
 
|full_id=C3251_granulocyte_Burkitt_acute_signet_diffuse_splenic_biphenotypic
 
|id=C3251
 
|id=C3251
|ontology_enrichment_celltype=CL:0000066!4.97e-10!254;CL:0000945!3.45e-08!24;CL:0000826!3.45e-08!24
+
|ontology_enrichment_celltype=CL:0000066!4.42e-09!253;CL:0000945!1.73e-08!24;CL:0000826!1.73e-08!24
|ontology_enrichment_disease=DOID:162!5.86e-27!235;DOID:14566!4.98e-26!239;DOID:2531!2.08e-20!51;DOID:0060083!2.08e-20!51;DOID:305!1.45e-17!106;DOID:1240!4.86e-16!39;DOID:0050687!3.31e-15!143;DOID:0050686!6.64e-15!137;DOID:8692!1.55e-12!31;DOID:0060058!6.51e-07!10
+
|ontology_enrichment_disease=DOID:162!1.69e-25!235;DOID:14566!1.28e-24!239;DOID:2531!2.52e-19!51;DOID:0060083!2.52e-19!51;DOID:305!6.33e-17!106;DOID:1240!6.45e-15!39;DOID:0050687!1.68e-14!143;DOID:0050686!2.84e-14!137;DOID:8692!1.13e-11!31;DOID:0060058!8.60e-07!10
|ontology_enrichment_uberon=UBERON:0001049!2.55e-09!57;UBERON:0005068!2.55e-09!57;UBERON:0006241!2.55e-09!57;UBERON:0007135!2.55e-09!57;UBERON:0001893!5.93e-09!34;UBERON:0002020!8.60e-09!34;UBERON:0003528!8.60e-09!34;UBERON:0002791!1.31e-08!33;UBERON:0001869!1.41e-08!32;UBERON:0000064!1.65e-08!219;UBERON:0002780!2.91e-08!41;UBERON:0001890!2.91e-08!41;UBERON:0006240!2.91e-08!41;UBERON:0003075!4.28e-08!86;UBERON:0007284!4.28e-08!86;UBERON:0002346!7.47e-08!90;UBERON:0003056!8.60e-08!61;UBERON:0003080!1.15e-07!42;UBERON:0000955!2.10e-07!69;UBERON:0006238!2.10e-07!69;UBERON:0000956!2.52e-07!25;UBERON:0000203!2.52e-07!25;UBERON:0000073!4.02e-07!94;UBERON:0001016!4.02e-07!94;UBERON:0005743!5.29e-07!86;UBERON:0002616!5.66e-07!59;UBERON:0001017!8.06e-07!82;UBERON:0002619!8.32e-07!22
+
|ontology_enrichment_uberon=UBERON:0011216!8.90e-11!223;UBERON:0001049!2.14e-09!56;UBERON:0005068!2.14e-09!56;UBERON:0006241!2.14e-09!56;UBERON:0007135!2.14e-09!56;UBERON:0001893!5.69e-09!34;UBERON:0000073!5.97e-09!53;UBERON:0002616!5.97e-09!53;UBERON:0003528!9.62e-09!34;UBERON:0002020!9.62e-09!34;UBERON:0001869!1.33e-08!32;UBERON:0000064!1.54e-08!218;UBERON:0002791!1.95e-08!32;UBERON:0003075!2.94e-08!82;UBERON:0007284!2.94e-08!82;UBERON:0003056!3.27e-08!61;UBERON:0002780!4.78e-08!41;UBERON:0001890!4.78e-08!41;UBERON:0003080!4.78e-08!41;UBERON:0006240!4.78e-08!41;UBERON:0002346!7.00e-08!86;UBERON:0010371!1.35e-07!104;UBERON:0000956!1.65e-07!25;UBERON:0000203!1.65e-07!25;UBERON:0000955!3.10e-07!68;UBERON:0006238!3.10e-07!68;UBERON:0001017!5.36e-07!81;UBERON:0002619!5.57e-07!22;UBERON:0001016!6.71e-07!89;UBERON:0001950!7.95e-07!20
 
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189355905436001!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323956757957376!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320783795722715!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00912943187882967!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319369758058221!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.046045304479977!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127735773897988!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139725247656327
 
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189355905436001!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323956757957376!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320783795722715!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00912943187882967!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319369758058221!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.046045304479977!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127735773897988!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139725247656327
 
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Revision as of 05:55, 19 October 2012


Full id: C3251_granulocyte_Burkitt_acute_signet_diffuse_splenic_biphenotypic



Phase1 CAGE Peaks

Hg19::chr12:125478179..125478208,+p1@BRI3BP
Hg19::chr12:125478212..125478235,+p3@BRI3BP
Hg19::chr12:125478241..125478260,+p2@BRI3BP


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell4.42e-09253
lymphocyte of B lineage1.73e-0824
pro-B cell1.73e-0824
Uber Anatomy
Ontology termp-valuen
organ system subdivision8.90e-11223
neural tube2.14e-0956
neural rod2.14e-0956
future spinal cord2.14e-0956
neural keel2.14e-0956
telencephalon5.69e-0934
regional part of nervous system5.97e-0953
regional part of brain5.97e-0953
brain grey matter9.62e-0934
gray matter9.62e-0934
cerebral hemisphere1.33e-0832
organ part1.54e-08218
regional part of telencephalon1.95e-0832
neural plate2.94e-0882
presumptive neural plate2.94e-0882
pre-chordal neural plate3.27e-0861
regional part of forebrain4.78e-0841
forebrain4.78e-0841
anterior neural tube4.78e-0841
future forebrain4.78e-0841
neurectoderm7.00e-0886
ecto-epithelium1.35e-07104
cerebral cortex1.65e-0725
pallium1.65e-0725
brain3.10e-0768
future brain3.10e-0768
central nervous system5.36e-0781
regional part of cerebral cortex5.57e-0722
nervous system6.71e-0789
neocortex7.95e-0720
Disease
Ontology termp-valuen
cancer1.69e-25235
disease of cellular proliferation1.28e-24239
hematologic cancer2.52e-1951
immune system cancer2.52e-1951
carcinoma6.33e-17106
leukemia6.45e-1539
cell type cancer1.68e-14143
organ system cancer2.84e-14137
myeloid leukemia1.13e-1131
lymphoma8.60e-0710


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#90536.336201576962630.003930750035764890.0189355905436001
E2F1#186934.907389214879320.008460985347239390.0323956757957376
E2F6#187635.017155731697390.00791769806886330.0320783795722715
EBF1#187938.9064668465690.00141523283560980.00912943187882967
EGR1#195834.988179094810140.008056488137383440.0319369758058221
ELF1#199734.258097958807540.01295179875054610.046045304479977
IRF1#365937.63716375356390.002244692747297240.0127735773897988
ZBTB7A#5134137.35190930787590.002516255860282270.0139725247656327



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.