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Coexpression cluster:C4239: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.64e-29!112;UBERON:0002390!1.77e-28!102;UBERON:0003061!1.77e-28!102;UBERON:0007023!7.72e-25!115;UBERON:0002371!8.48e-20!80;UBERON:0001474!1.42e-18!86;UBERON:0002405!3.15e-18!115;UBERON:0004765!8.93e-13!101;UBERON:0001434!8.93e-13!101;UBERON:0001049!2.77e-08!57;UBERON:0005068!2.77e-08!57;UBERON:0006241!2.77e-08!57;UBERON:0007135!2.77e-08!57;UBERON:0000178!1.25e-07!15;UBERON:0000179!1.25e-07!15;UBERON:0000463!1.25e-07!15;UBERON:0003080!4.59e-07!42;UBERON:0002780!8.39e-07!41;UBERON:0001890!8.39e-07!41;UBERON:0006240!8.39e-07!41
|ontology_enrichment_uberon=UBERON:0002193!1.64e-29!112;UBERON:0002390!1.77e-28!102;UBERON:0003061!1.77e-28!102;UBERON:0007023!7.72e-25!115;UBERON:0002371!8.48e-20!80;UBERON:0001474!1.42e-18!86;UBERON:0002405!3.15e-18!115;UBERON:0004765!8.93e-13!101;UBERON:0001434!8.93e-13!101;UBERON:0001049!2.77e-08!57;UBERON:0005068!2.77e-08!57;UBERON:0006241!2.77e-08!57;UBERON:0007135!2.77e-08!57;UBERON:0000178!1.25e-07!15;UBERON:0000179!1.25e-07!15;UBERON:0000463!1.25e-07!15;UBERON:0003080!4.59e-07!42;UBERON:0002780!8.39e-07!41;UBERON:0001890!8.39e-07!41;UBERON:0006240!8.39e-07!41
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280275771442043!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323216255712169!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00917305915212886!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.032152988825717!IRF4#3662;2:14.6096751244961:0.00605612247321789:0.02684957231313!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195179560880483!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173300094389884!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00883727321608594!REST#5978;3:9.65002871612802:0.00111263624711459:0.00769451840897899!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457711614066948!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630404510282955!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329270049555222!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109697774721027
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}}
}}

Revision as of 12:36, 5 September 2012


Full id: C4239_Mast_Eosinophils_Neutrophils_CD19_CD4_granulocyte_immature



Phase1 CAGE Peaks

Hg19::chr2:61108650..61108687,+p2@REL
Hg19::chr7:37488426..37488437,-p10@ELMO1
Hg19::chr7:37488448..37488517,-p1@ELMO1


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:0006911phagocytosis, engulfment0.0211914288769233
GO:0016601Rac protein signal transduction0.0211914288769233
GO:0017124SH3 domain binding0.0313896259573782
GO:0006909phagocytosis0.0482466287112283



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
hematopoietic stem cell1.57e-51172
angioblastic mesenchymal cell1.57e-51172
leukocyte6.08e-49140
hematopoietic oligopotent progenitor cell4.77e-48165
hematopoietic multipotent progenitor cell4.77e-48165
hematopoietic cell8.24e-47182
hematopoietic lineage restricted progenitor cell3.88e-38124
nongranular leukocyte5.35e-36119
myeloid cell1.44e-31112
common myeloid progenitor1.44e-31112
myeloid leukocyte2.48e-2776
granulocyte monocyte progenitor cell2.16e-2471
myeloid lineage restricted progenitor cell4.03e-2270
macrophage dendritic cell progenitor1.03e-2065
monopoietic cell1.66e-1963
monocyte1.66e-1963
monoblast1.66e-1963
promonocyte1.66e-1963
CD14-positive, CD16-negative classical monocyte4.67e-1942
classical monocyte3.74e-1645
lymphocyte2.54e-1453
common lymphoid progenitor2.54e-1453
lymphoid lineage restricted progenitor cell3.74e-1452
mature alpha-beta T cell1.19e-0818
alpha-beta T cell1.19e-0818
immature T cell1.19e-0818
mature T cell1.19e-0818
immature alpha-beta T cell1.19e-0818
T cell5.68e-0825
pro-T cell5.68e-0825
dendritic cell1.44e-0710
B cell4.97e-0714
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.64e-29112
hematopoietic system1.77e-28102
blood island1.77e-28102
adult organism7.72e-25115
bone marrow8.48e-2080
bone element1.42e-1886
immune system3.15e-18115
skeletal element8.93e-13101
skeletal system8.93e-13101
neural tube2.77e-0857
neural rod2.77e-0857
future spinal cord2.77e-0857
neural keel2.77e-0857
blood1.25e-0715
haemolymphatic fluid1.25e-0715
organism substance1.25e-0715
anterior neural tube4.59e-0742
regional part of forebrain8.39e-0741
forebrain8.39e-0741
future forebrain8.39e-0741


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
CTCF#1066435.360256373075030.0064925092527670.0280275771442043
E2F6#187635.017155731697390.00791769806886330.0323216255712169
EBF1#187938.9064668465690.00141523283560980.00917305915212886
EGR1#195834.988179094810140.008056488137383440.032152988825717
IRF4#3662214.60967512449610.006056122473217890.02684957231313
MEF2A#4205318.74323090964410.0001518243905622470.00195179560880483
PAX5#507936.669565531177830.003370290999677260.0173300094389884
POU2F2#545239.106124057742520.001324165192682130.00883727321608594
REST#597839.650028716128020.001112636247114590.00769451840897899
SMC3#9126210.02995522995520.0126656379767470.0457711614066948
TCF12#6938310.63446490218640.0008313523990202070.00630404510282955
TRIM28#10155212.39368336350830.008368344129438470.0329270049555222
ZNF263#1012738.221841637010680.001799043925565870.0109697774721027



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.