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Coexpression cluster:C489: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:24, 17 September 2013


Full id: C489_immature_CD14_Natural_Basophils_CD8_CD4_CD34



Phase1 CAGE Peaks

Hg19::chr10:17067939..17067950,+p@chr10:17067939..17067950
+
Hg19::chr10:3845786..3845804,+p@chr10:3845786..3845804
+
Hg19::chr11:62310904..62310918,+p@chr11:62310904..62310918
+
Hg19::chr11:62310937..62310946,+p@chr11:62310937..62310946
+
Hg19::chr11:62310952..62310964,+p@chr11:62310952..62310964
+
Hg19::chr11:62310973..62311002,+p@chr11:62310973..62311002
+
Hg19::chr11:62321754..62321778,+p@chr11:62321754..62321778
+
Hg19::chr12:122228579..122228598,+p@chr12:122228579..122228598
+
Hg19::chr12:72056594..72056607,-p@chr12:72056594..72056607
-
Hg19::chr15:86125585..86125597,+p@chr15:86125585..86125597
+
Hg19::chr17:7746945..7746958,+p@chr17:7746945..7746958
+
Hg19::chr19:56146912..56146939,-p@chr19:56146912..56146939
-
Hg19::chr22:20862211..20862230,-p@chr22:20862211..20862230
-
Hg19::chr22:20862231..20862254,-p@chr22:20862231..20862254
-
Hg19::chr3:33758833..33758853,+p@chr3:33758833..33758853
+
Hg19::chr6:136610032..136610051,+p@chr6:136610032..136610051
+
Hg19::chr6:16699696..16699707,-p@chr6:16699696..16699707
-
Hg19::chr6:16699727..16699740,-p@chr6:16699727..16699740
-
Hg19::chr6:293545..293553,-p@chr6:293545..293553
-


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 monocyte1.01e-8542
CD14-positive, CD16-negative classical monocyte1.01e-8542
defensive cell8.75e-7448
phagocyte8.75e-7448
leukocyte7.95e-72136
granulocyte monocyte progenitor cell1.58e-6967
myeloid leukocyte1.69e-6772
macrophage dendritic cell progenitor7.49e-6661
myeloid lineage restricted progenitor cell5.27e-6366
hematopoietic lineage restricted progenitor cell9.34e-63120
monopoietic cell2.02e-6059
monocyte2.02e-6059
monoblast2.02e-6059
promonocyte2.02e-6059
nongranular leukocyte4.59e-60115
hematopoietic stem cell1.11e-55168
angioblastic mesenchymal cell1.11e-55168
hematopoietic cell3.48e-52177
hematopoietic oligopotent progenitor cell4.29e-52161
hematopoietic multipotent progenitor cell4.29e-52161
myeloid cell8.43e-49108
common myeloid progenitor8.43e-49108
stuff accumulating cell5.98e-4187
mesenchymal cell2.24e-21354
connective tissue cell1.08e-20361
motile cell2.69e-18386
multi fate stem cell2.30e-15427
stem cell2.48e-15441
somatic stem cell5.85e-15433
intermediate monocyte5.37e-129
CD14-positive, CD16-positive monocyte5.37e-129
natural killer cell5.64e-113
pro-NK cell5.64e-113
basophil7.54e-113
single nucleate cell1.54e-093
mononuclear cell1.54e-093
CD4-positive, alpha-beta T cell2.16e-086
CD1a-positive Langerhans cell4.97e-082
immature CD1a-positive Langerhans cell4.97e-082
mature alpha-beta T cell1.06e-0718
alpha-beta T cell1.06e-0718
immature T cell1.06e-0718
mature T cell1.06e-0718
immature alpha-beta T cell1.06e-0718
somatic cell2.95e-07588
Uber Anatomy
Ontology termp-valuen
bone marrow4.07e-6076
bone element5.61e-5582
hematopoietic system8.06e-5298
blood island8.06e-5298
skeletal element3.51e-4990
immune system2.92e-4793
hemolymphoid system5.18e-46108
skeletal system3.15e-43100
musculoskeletal system1.08e-21167
connective tissue9.12e-20371
lateral plate mesoderm2.56e-19203
mesoderm1.14e-08315
mesoderm-derived structure1.14e-08315
presumptive mesoderm1.14e-08315


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)
MA0003.10.000581566
MA0004.10.563888
MA0006.10.638512
MA0007.10.180248
MA0009.10.580032
MA0014.10.00883981
MA0017.10.367718
MA0019.10.305657
MA0024.10.485346
MA0025.10.70396
MA0027.12.15732
MA0028.10.332468
MA0029.10.50258
MA0030.10.492344
MA0031.11.11067
MA0038.10.269828
MA0040.10.507819
MA0041.10.206566
MA0042.10.183918
MA0043.10.580321
MA0046.10.570066
MA0048.10.0472517
MA0050.10.184533
MA0051.10.266537
MA0052.10.511289
MA0055.10.106762
MA0056.10
MA0057.10.00844127
MA0058.10.12994
MA0059.10.129144
MA0060.10.152097
MA0061.10.535933
MA0063.10
MA0066.13.82398
MA0067.10.879057
MA0068.10.994655
MA0069.10.566544
MA0070.10.556335
MA0071.10.240074
MA0072.12.33267
MA0073.10.0165687
MA0074.10.734236
MA0076.10.139892
MA0077.10.545231
MA0078.10.915792
MA0081.10.129245
MA0083.10.586921
MA0084.11.06048
MA0087.10.550016
MA0088.10.0542435
MA0089.10
MA0090.10.149167
MA0091.13.1902
MA0092.10.168981
MA0093.10.646398
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.654976
MA0103.10.295078
MA0105.10.88329
MA0106.12.2623
MA0107.10.46886
MA0108.20.432749
MA0109.10
MA0111.10.15804
MA0113.10.315797
MA0114.10.456488
MA0115.11.88888
MA0116.10.219141
MA0117.10.614633
MA0119.10.119385
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.27535
MA0139.11.15415
MA0140.10.669735
MA0141.10.128074
MA0142.10.407878
MA0143.10.847678
MA0144.10.422223
MA0145.10.0209869
MA0146.10.0059432
MA0147.10.223797
MA0148.11.14208
MA0149.10.230803
MA0062.20.027823
MA0035.21.24312
MA0039.20.00287338
MA0138.20.347473
MA0002.21.32966
MA0137.20.697429
MA0104.20.151208
MA0047.20.292798
MA0112.20.00303039
MA0065.20.468021
MA0150.11.40955
MA0151.10
MA0152.10.243034
MA0153.10.67139
MA0154.10.214105
MA0155.10.0530942
MA0156.10.106343
MA0157.10.384449
MA0158.10
MA0159.10.487475
MA0160.10.222325
MA0161.10
MA0162.10.021183
MA0163.10.0262946
MA0164.10.870085
MA0080.20.31321
MA0018.20.30364
MA0099.21.26491
MA0079.29.24127e-11
MA0102.21.09681
MA0258.10.706831
MA0259.10.235101
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#10664113.103306321253960.0001618769715296470.00201456971277226
CTCFL#14069044.157152496626180.01381538141971840.048596026408473
FOS#235383.788612761639750.0005646531665148650.00481717138193481
HNF4A#317244.869955865884990.00802670606715890.0321841730313667
SMC3#912664.751031424715640.001097208282891840.00766445962523849



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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