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Coexpression cluster:C4239: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4239_Mast_Eosinophils_Neutrophils_CD19_CD4_granulocyte_immature
|id=C4239
}}

Latest revision as of 12:42, 17 September 2013


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 cell2.56e-54168
angioblastic mesenchymal cell2.56e-54168
leukocyte1.37e-52136
hematopoietic oligopotent progenitor cell8.16e-51161
hematopoietic multipotent progenitor cell8.16e-51161
hematopoietic cell6.17e-49177
hematopoietic lineage restricted progenitor cell1.95e-41120
nongranular leukocyte1.69e-39115
myeloid cell4.68e-34108
common myeloid progenitor4.68e-34108
myeloid leukocyte8.46e-3172
granulocyte monocyte progenitor cell9.15e-2867
myeloid lineage restricted progenitor cell1.68e-2566
macrophage dendritic cell progenitor3.99e-2461
monopoietic cell7.20e-2359
monocyte7.20e-2359
monoblast7.20e-2359
promonocyte7.20e-2359
defensive cell6.40e-2148
phagocyte6.40e-2148
classical monocyte2.44e-1942
CD14-positive, CD16-negative classical monocyte2.44e-1942
lymphocyte1.55e-1453
common lymphoid progenitor1.55e-1453
nucleate cell2.33e-1455
lymphoid lineage restricted progenitor cell3.50e-1452
mature alpha-beta T cell3.08e-0818
alpha-beta T cell3.08e-0818
immature T cell3.08e-0818
mature T cell3.08e-0818
immature alpha-beta T cell3.08e-0818
B cell1.10e-0714
dendritic cell1.19e-0710
T cell2.05e-0725
pro-T cell2.05e-0725
Uber Anatomy
Ontology termp-valuen
hemolymphoid system4.71e-31108
hematopoietic system4.06e-3098
blood island4.06e-3098
immune system1.57e-2593
adult organism1.68e-25114
bone marrow1.59e-2276
bone element2.93e-2182
skeletal element6.03e-1790
skeletal system1.44e-13100
neural tube6.07e-1056
neural rod6.07e-1056
future spinal cord6.07e-1056
neural keel6.07e-1056
regional part of nervous system4.19e-0953
regional part of brain4.19e-0953
regional part of forebrain2.64e-0841
forebrain2.64e-0841
anterior neural tube2.64e-0841
future forebrain2.64e-0841
central nervous system1.32e-0781
lateral plate mesoderm3.27e-07203
telencephalon9.23e-0734
brain9.95e-0768
future brain9.95e-0768


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)
MA0003.12.61626
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.12.99448
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.14.18141
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.12.53618
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.15.21222
MA0163.11.84145
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.941469
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



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.

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