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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:47, 17 September 2013


Full id: C1560_CD14_Dendritic_Macrophage_dura_Monocytederived_lymph_left



Phase1 CAGE Peaks

Hg19::chr10:105610433..105610453,-p@chr10:105610433..105610453
-
Hg19::chr11:117860734..117860750,+p@chr11:117860734..117860750
+
Hg19::chr17:6983594..6983619,-p2@CLEC10A
Hg19::chr19:7812446..7812473,-p3@CD209
Hg19::chr19:7812475..7812509,-p1@CD209


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:0010324membrane invagination0.00108911619621619
GO:0006897endocytosis0.00108911619621619
GO:0016044membrane organization and biogenesis0.00108911619621619
GO:0005529sugar binding0.00108911619621619
GO:0046795intracellular virion transport0.00108911619621619
GO:0046794virion transport0.00108911619621619
GO:0046968peptide antigen transport0.00108911619621619
GO:0042607exogenous peptide antigen binding0.00108911619621619
GO:0019062virion attachment to host cell surface receptor0.00145213355452384
GO:0030246carbohydrate binding0.00146200395893184
GO:0046790virion binding0.00195906581209551
GO:0016192vesicle-mediated transport0.00195906581209551
GO:0007159leukocyte adhesion0.00208325063589046
GO:0044409entry into host0.00208325063589046
GO:0030260entry into host cell0.00208325063589046
GO:0046718entry of virus into host cell0.00208325063589046
GO:0007157heterophilic cell adhesion0.00208325063589046
GO:0052126movement in host environment0.00208325063589046
GO:0019048virus-host interaction0.00208325063589046
GO:0051828entry into other organism during symbiotic interaction0.00208325063589046
GO:0019059initiation of viral infection0.00208325063589046
GO:0051806entry into cell of other organism during symbiotic interaction0.00208325063589046
GO:0052192movement in environment of other organism during symbiotic interaction0.00208325063589046
GO:0005537mannose binding0.00217791178596612
GO:0009405pathogenesis0.00226499491433228
GO:0009988cell-cell recognition0.00234537440810924
GO:0048029monosaccharide binding0.0027423537189971
GO:0042605peptide antigen binding0.0027999249712539
GO:0006955immune response0.00312321995174038
GO:0051701interaction with host0.00319380039659979
GO:0002376immune system process0.00394647724338942
GO:0019079viral genome replication0.00394647724338942
GO:0044403symbiosis, encompassing mutualism through parasitism0.00409839166688678
GO:0044419interspecies interaction between organisms0.00409839166688678
GO:0008037cell recognition0.00471693332176563
GO:0015833peptide transport0.00471693332176563
GO:0019058viral infectious cycle0.00588295535511979
GO:0022415viral reproductive process0.00652940717060383
GO:0048002antigen processing and presentation of peptide antigen0.0117111623236994
GO:0016043cellular component organization and biogenesis0.0172092766472403
GO:0003823antigen binding0.0187587343868919
GO:0042277peptide binding0.0215094572875855
GO:0005886plasma membrane0.0217088453958351
GO:0006810transport0.0237207834844514
GO:0051234establishment of localization0.0243576701727509
GO:0051179localization0.0279832014671252
GO:0022414reproductive process0.0281445955333581
GO:0051704multi-organism process0.0300757319177876
GO:0016337cell-cell adhesion0.0306942244842114
GO:0019882antigen processing and presentation0.0359388563332375



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
monopoietic cell7.70e-3759
monocyte7.70e-3759
monoblast7.70e-3759
promonocyte7.70e-3759
macrophage dendritic cell progenitor2.92e-3561
myeloid leukocyte9.78e-3272
myeloid lineage restricted progenitor cell9.83e-3266
granulocyte monocyte progenitor cell4.31e-3167
defensive cell8.43e-3048
phagocyte8.43e-3048
classical monocyte1.38e-2042
CD14-positive, CD16-negative classical monocyte1.38e-2042
myeloid cell2.71e-17108
common myeloid progenitor2.71e-17108
nongranular leukocyte1.99e-16115
leukocyte6.31e-14136
macrophage2.62e-136
hematopoietic lineage restricted progenitor cell1.37e-12120
stuff accumulating cell2.24e-1287
hematopoietic stem cell3.54e-09168
angioblastic mesenchymal cell3.54e-09168
hematopoietic cell3.48e-08177
hematopoietic oligopotent progenitor cell3.63e-08161
hematopoietic multipotent progenitor cell3.63e-08161
adult endothelial progenitor cell1.07e-073
intermediate monocyte8.94e-079
CD14-positive, CD16-positive monocyte8.94e-079
Uber Anatomy
Ontology termp-valuen
bone marrow4.44e-2676
immune system5.55e-2693
hematopoietic system3.83e-2598
blood island3.83e-2598
hemolymphoid system2.71e-24108
adult organism4.52e-24114
bone element2.34e-2382
skeletal element2.65e-2090
skeletal system3.43e-17100
lateral plate mesoderm4.45e-15203
organ1.75e-10503
mesoderm1.39e-09315
mesoderm-derived structure1.39e-09315
presumptive mesoderm1.39e-09315
musculoskeletal system8.59e-09167
multi-cellular organism2.87e-08656
developing anatomical structure8.28e-08581
embryonic structure8.91e-08564
embryo9.95e-08592
anatomical system1.14e-07624
anatomical group1.28e-07625
germ layer1.65e-07560
germ layer / neural crest1.65e-07560
embryonic tissue1.65e-07560
presumptive structure1.65e-07560
germ layer / neural crest derived structure1.65e-07560
epiblast (generic)1.65e-07560
cardiac chamber3.68e-073
valve9.15e-073
cardiac mesenchyme9.15e-073
cardial valve9.15e-073
tunica intima9.15e-073
heart layer9.15e-073
endocardium9.15e-073
endocardial cushion9.15e-073
presumptive endocardium9.15e-073


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)
MA0003.10.0497246
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.11.01397
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.362215
MA0074.11.73427
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.11.76306
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.11.76068
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.11.67417
MA0145.10.143698
MA0146.10.143081
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.20.0575907
MA0138.20.837782
MA0002.20.30855
MA0137.21.20193
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.12.09554
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.24.06591
MA0018.20.781393
MA0099.20.699641
MA0079.20.00732454
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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

No analysis results for this cluster

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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