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

Latest revision as of 11:33, 17 September 2013


Full id: C897_melanoma_Melanocyte_CD14_Macrophage_retina_myxofibrosarcoma_Monocytederived



Phase1 CAGE Peaks

Hg19::chr12:56361058..56361072,+p14@CDK2
Hg19::chr15:33446896..33446905,-p@chr15:33446896..33446905
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Hg19::chr15:33446939..33446959,-p@chr15:33446939..33446959
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Hg19::chr15:33446964..33446978,-p@chr15:33446964..33446978
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Hg19::chr15:33446981..33446997,-p@chr15:33446981..33446997
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Hg19::chr15:33446999..33447010,-p@chr15:33446999..33447010
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Hg19::chr15:33447022..33447035,-p@chr15:33447022..33447035
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Hg19::chr15:33447055..33447064,-p@chr15:33447055..33447064
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Hg19::chr2:12454437..12454450,+p1@ENST00000412606


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:0035173histone kinase activity0.00226657247144707
GO:0007089traversing start control point of mitotic cell cycle0.00566643117861768
GO:0000307cyclin-dependent protein kinase holoenzyme complex0.0060441932571922
GO:0000086G2/M transition of mitotic cell cycle0.00717747949291573
GO:0000080G1 phase of mitotic cell cycle0.00717747949291573
GO:0051318G1 phase0.00717747949291573
GO:0006275regulation of DNA replication0.00805892434292293
GO:0004693cyclin-dependent protein kinase activity0.00805892434292293
GO:0007346regulation of progression through mitotic cell cycle0.00805892434292293
GO:0051052regulation of DNA metabolic process0.0111062051100907
GO:0051329interphase of mitotic cell cycle0.016999293535853
GO:0051325interphase0.016999293535853
GO:0006261DNA-dependent DNA replication0.0287680352145205
GO:0008284positive regulation of cell proliferation0.0326653091473255
GO:0007067mitosis0.0326653091473255
GO:0000087M phase of mitotic cell cycle0.0326653091473255
GO:0051301cell division0.0326653091473255
GO:0000279M phase0.0348485517484987
GO:0000278mitotic cell cycle0.0348485517484987
GO:0000074regulation of progression through cell cycle0.0348485517484987
GO:0006260DNA replication0.0348485517484987
GO:0051726regulation of cell cycle0.0348485517484987
GO:0042802identical protein binding0.0348485517484987
GO:0022403cell cycle phase0.0348485517484987
GO:0042127regulation of cell proliferation0.0425208995643471



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
defensive cell4.67e-4048
phagocyte4.67e-4048
monopoietic cell2.31e-3859
monocyte2.31e-3859
monoblast2.31e-3859
promonocyte2.31e-3859
macrophage dendritic cell progenitor1.09e-3661
classical monocyte3.12e-3642
CD14-positive, CD16-negative classical monocyte3.12e-3642
myeloid lineage restricted progenitor cell5.97e-3366
granulocyte monocyte progenitor cell2.86e-3267
myeloid leukocyte3.73e-2972
stuff accumulating cell1.53e-2787
nongranular leukocyte1.12e-15115
myeloid cell2.12e-15108
common myeloid progenitor2.12e-15108
hematopoietic lineage restricted progenitor cell1.01e-12120
leukocyte1.92e-11136
melanocyte1.89e-0910
melanoblast1.89e-0910
hematopoietic stem cell3.17e-07168
angioblastic mesenchymal cell3.17e-07168
adult endothelial progenitor cell4.83e-073
light melanocyte5.21e-073
hematopoietic oligopotent progenitor cell7.43e-07161
hematopoietic multipotent progenitor cell7.43e-07161
Uber Anatomy
Ontology termp-valuen
bone marrow1.49e-2876
bone element2.34e-2882
hematopoietic system1.36e-2598
blood island1.36e-2598
immune system7.31e-2593
skeletal element1.17e-2490
hemolymphoid system6.20e-22108
skeletal system6.88e-21100
adult organism6.73e-15114
neural tube8.93e-1456
neural rod8.93e-1456
future spinal cord8.93e-1456
neural keel8.93e-1456
regional part of nervous system3.10e-1253
regional part of brain3.10e-1253
brain1.32e-1068
future brain1.32e-1068
central nervous system1.59e-1081
nervous system3.05e-1089
musculoskeletal system4.17e-10167
neural plate9.05e-1082
presumptive neural plate9.05e-1082
organ5.34e-09503
neurectoderm5.75e-0986
brain grey matter1.45e-0834
gray matter1.45e-0834
regional part of forebrain2.73e-0841
forebrain2.73e-0841
anterior neural tube2.73e-0841
future forebrain2.73e-0841
telencephalon2.80e-0834
neural nucleus5.83e-089
nucleus of brain5.83e-089
ecto-epithelium1.15e-07104
germ layer1.16e-07560
germ layer / neural crest1.16e-07560
embryonic tissue1.16e-07560
presumptive structure1.16e-07560
germ layer / neural crest derived structure1.16e-07560
epiblast (generic)1.16e-07560
embryonic structure1.95e-07564
posterior neural tube2.19e-0715
chordal neural plate2.19e-0715
developing anatomical structure2.34e-07581
lateral plate mesoderm6.63e-07203
regional part of telencephalon7.02e-0732
embryo9.24e-07592
brainstem9.35e-076


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)
MA0003.10.000472949
MA0004.10.415381
MA0006.10.265592
MA0007.14.79398
MA0009.10.870971
MA0014.10.0956087
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.12.15039
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.0199484
MA0056.10
MA0057.10.0725989
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.0776172
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.11.55973
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.14.34987
MA0089.10
MA0090.11.66392
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.552298
MA0145.10.177438
MA0146.10.0045741
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.421263
MA0035.20.473658
MA0039.20.0006485
MA0138.20.608783
MA0002.22.0863
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.22.52701
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.0402662
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.11.14546
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.034916
MA0164.10.583138
MA0080.21.35856
MA0018.20.556211
MA0099.20.481058
MA0079.23.47892e-06
MA0102.21.41188
MA0258.11.61512
MA0259.10.218904
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
EP300#203375.268621342618044.17034622553318e-050.0007557639934903
USF1#739174.947832771161756.35032938033638e-050.00103563718012641
YY1#752873.819799472108550.0003529672812141940.00353675044447177



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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