Personal tools

Coexpression cluster:C293: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:15, 17 September 2013


Full id: C293_CD14_CD14CD16_Basophils_Peripheral_immature_Eosinophils_CD34



Phase1 CAGE Peaks

Hg19::chr10:104563028..104563065,-p@chr10:104563028..104563065
-
Hg19::chr11:10921577..10921613,+p@chr11:10921577..10921613
+
Hg19::chr11:109898250..109898258,+p@chr11:109898250..109898258
+
Hg19::chr11:503682..503702,+p@chr11:503682..503702
+
Hg19::chr12:116996410..116996424,+p@chr12:116996410..116996424
+
Hg19::chr12:69004435..69004453,-p@chr12:69004435..69004453
-
Hg19::chr13:41591558..41591570,+p@chr13:41591558..41591570
+
Hg19::chr15:67385901..67385913,-p@chr15:67385901..67385913
-
Hg19::chr15:67402220..67402236,+p@chr15:67402220..67402236
+
Hg19::chr16:11892467..11892492,-p@chr16:11892467..11892492
-
Hg19::chr17:7036438..7036444,+p@chr17:7036438..7036444
+
Hg19::chr17:79790192..79790220,+p@chr17:79790192..79790220
+
Hg19::chr17:81147275..81147285,-p@chr17:81147275..81147285
-
Hg19::chr17:81147409..81147425,-p@chr17:81147409..81147425
-
Hg19::chr17:81148156..81148167,-p@chr17:81148156..81148167
-
Hg19::chr17:8856790..8856815,+p@chr17:8856790..8856815
+
Hg19::chr1:234535009..234535013,+p@chr1:234535009..234535013
+
Hg19::chr1:236230397..236230414,+p@chr1:236230397..236230414
+
Hg19::chr1:27986166..27986179,-p@chr1:27986166..27986179
-
Hg19::chr1:42230480..42230491,+p@chr1:42230480..42230491
+
Hg19::chr22:44464675..44464690,-p@chr22:44464675..44464690
-
Hg19::chr22:50743236..50743253,+p@chr22:50743236..50743253
+
Hg19::chr2:10169430..10169492,+p@chr2:10169430..10169492
+
Hg19::chr2:145273135..145273151,-p@chr2:145273135..145273151
-
Hg19::chr2:145440056..145440091,+p@chr2:145440056..145440091
+
Hg19::chr2:145440766..145440771,-p@chr2:145440766..145440771
-
Hg19::chr2:145441152..145441172,+p@chr2:145441152..145441172
+
Hg19::chr2:145441185..145441198,+p@chr2:145441185..145441198
+
Hg19::chr2:208366677..208366692,-p@chr2:208366677..208366692
-
Hg19::chr2:238603376..238603380,+p@chr2:238603376..238603380
+
Hg19::chr2:243028282..243028329,+p@chr2:243028282..243028329
+
Hg19::chr3:148863449..148863470,+p@chr3:148863449..148863470
+
Hg19::chr3:188118437..188118443,+p@chr3:188118437..188118443
+
Hg19::chr4:130015616..130015630,-p@chr4:130015616..130015630
-
Hg19::chr4:148604535..148604547,+p@chr4:148604535..148604547
+
Hg19::chr4:159731587..159731603,+p@chr4:159731587..159731603
+
Hg19::chr4:2788911..2788937,-p@chr4:2788911..2788937
-
Hg19::chr4:3374939..3374950,+p@chr4:3374939..3374950
+
Hg19::chr5:100237661..100237690,-p@chr5:100237661..100237690
-
Hg19::chr5:159846453..159846490,+p@chr5:159846453..159846490
+
Hg19::chr5:169757791..169757802,+p@chr5:169757791..169757802
+
Hg19::chr6:12052345..12052360,+p@chr6:12052345..12052360
+
Hg19::chr9:90216271..90216293,-p@chr9:90216271..90216293
-


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 monocyte9.29e-13142
CD14-positive, CD16-negative classical monocyte9.29e-13142
defensive cell3.87e-11348
phagocyte3.87e-11348
myeloid leukocyte1.09e-10372
granulocyte monocyte progenitor cell3.73e-9767
myeloid lineage restricted progenitor cell1.95e-9466
macrophage dendritic cell progenitor6.22e-9461
monopoietic cell6.85e-9359
monocyte6.85e-9359
monoblast6.85e-9359
promonocyte6.85e-9359
leukocyte5.90e-76136
myeloid cell1.25e-68108
common myeloid progenitor1.25e-68108
nongranular leukocyte1.63e-63115
hematopoietic lineage restricted progenitor cell1.79e-62120
hematopoietic stem cell2.47e-59168
angioblastic mesenchymal cell2.47e-59168
stuff accumulating cell7.75e-5887
hematopoietic cell9.83e-56177
hematopoietic oligopotent progenitor cell9.04e-53161
hematopoietic multipotent progenitor cell9.04e-53161
intermediate monocyte9.35e-339
CD14-positive, CD16-positive monocyte9.35e-339
mesenchymal cell6.00e-22354
connective tissue cell2.74e-21361
motile cell5.80e-19386
stem cell3.97e-16441
multi fate stem cell4.06e-16427
somatic stem cell1.00e-15433
non-classical monocyte7.09e-123
CD14-low, CD16-positive monocyte7.09e-123
basophil7.61e-123
single nucleate cell3.82e-113
mononuclear cell3.82e-113
natural killer cell6.10e-103
pro-NK cell6.10e-103
somatic cell3.12e-08588
granulocyte2.33e-078
Uber Anatomy
Ontology termp-valuen
bone marrow1.58e-8476
bone element1.25e-7782
hematopoietic system4.49e-7398
blood island4.49e-7398
skeletal element7.55e-7090
immune system2.85e-6793
hemolymphoid system2.44e-65108
skeletal system7.46e-62100
musculoskeletal system7.83e-33167
lateral plate mesoderm1.18e-29203
connective tissue2.18e-20371
mesoderm3.83e-15315
mesoderm-derived structure3.83e-15315
presumptive mesoderm3.83e-15315


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)
MA0003.10.00170961
MA0004.11.51017
MA0006.10.142277
MA0007.10.154321
MA0009.10.302111
MA0014.10.00352503
MA0017.10.192742
MA0019.10.104216
MA0024.10.227674
MA0025.10.406058
MA0027.11.80451
MA0028.10.0607524
MA0029.10.240834
MA0030.10.232995
MA0031.10.190676
MA0038.10.283779
MA0040.10.244872
MA0041.10.190367
MA0042.10.364423
MA0043.10.302346
MA0046.10.294047
MA0048.10.0624983
MA0050.10.366018
MA0051.10.278721
MA0052.10.247554
MA0055.10.625791
MA0056.10
MA0057.10.00972432
MA0058.12.36426
MA0059.11.03884
MA0060.10.0110214
MA0061.11.01922
MA0063.10
MA0066.10.0836468
MA0067.10.561712
MA0068.10.241376
MA0069.10.291208
MA0070.10.283018
MA0071.10.0674977
MA0072.10.279748
MA0073.10.366741
MA0074.10.0813134
MA0076.10.0241147
MA0077.10.274171
MA0078.10.129652
MA0081.11.03959
MA0083.10.307714
MA0084.10.730117
MA0087.10.277975
MA0088.10.0911957
MA0089.10
MA0090.11.18863
MA0091.10.045895
MA0092.10.325996
MA0093.12.31412
MA0095.10
MA0098.10
MA0100.10.300645
MA0101.11.47497
MA0103.10.131452
MA0105.10.0794316
MA0106.10.10234
MA0107.11.31583
MA0108.20.552897
MA0109.10
MA0111.10.298254
MA0113.10.356293
MA0114.10.156479
MA0115.10.495652
MA0116.10.737268
MA0117.10.33048
MA0119.10.394288
MA0122.10.350462
MA0124.10.460583
MA0125.10.391616
MA0130.10
MA0131.10.139545
MA0132.10
MA0133.10
MA0135.10.324957
MA0136.10.609654
MA0139.10.329932
MA0140.11.31447
MA0141.10.224411
MA0142.10.98257
MA0143.10.722292
MA0144.10.0181205
MA0145.10.070624
MA0146.10.000289598
MA0147.11.04041
MA0148.10.435932
MA0149.10.225137
MA0062.20.0590197
MA0035.20.869365
MA0039.20.101132
MA0138.20.130311
MA0002.21.78968
MA0137.20.0644806
MA0104.21.23451
MA0047.21.09401
MA0112.20.244919
MA0065.20.0406788
MA0150.10.26659
MA0151.10
MA0152.10.243188
MA0153.10.985783
MA0154.10.208917
MA0155.10.143139
MA0156.10.343133
MA0157.10.469945
MA0158.10
MA0159.10.757773
MA0160.10.465642
MA0161.10
MA0162.10.0154432
MA0163.10.147424
MA0164.10.75029
MA0080.21.45333
MA0018.20.687976
MA0099.20.243592
MA0079.24.83676e-11
MA0102.20.764449
MA0258.10.051571
MA0259.10.545724
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
BATF#1053873.965223547584310.00172000239750150.0106652811490031
BCL11A#5333585.278038158810620.0001140276771569360.00156100885759513
EBF1#1879183.728288447400982.96527101020769e-071.49753355432824e-05
MEF2A#420593.923001818297590.0003757219878006550.00373287944101148
MEF2C#420865.764375045482430.0005669836506498940.00483389432573259
SPI1#6688173.24356975918345.14672540128264e-060.000157861631184892
USF1#7391142.071185811183990.004714302297936050.0222222882151175



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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C293&oldid=3067411"