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Coexpression cluster:C1299: Difference between revisions

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{{Coexpression_clusters
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1;0.629368,MA0153.1;1.13732,MA0154.1;0.413181,MA0155.1;0.318517,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.150673,MA0163.1;0.508943,MA0164.1;1.74929,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.476723,MA0102.2;1.58513,MA0258.1;0.788656,MA0259.1;0.893594,MA0442.1;0}}
|full_id=C1299_chronic_acute_chorionic_leukemia_choriocarcinoma_pancreatic_placenta
|gostat_on_coexpression_clusters=GO:0019901!protein kinase binding!0.0189420699399505!387778$GO:0019900!kinase binding!0.0189420699399505!387778$GO:0019899!enzyme binding!0.0389045880921543!387778
|id=C1299
|ontology_enrichment_celltype=CL:0000763!7.27e-46!112;CL:0000049!7.27e-46!112;CL:0000037!1.62e-36!172;CL:0000566!1.62e-36!172;CL:0000988!3.95e-36!182;CL:0002032!8.55e-36!165;CL:0000837!8.55e-36!165;CL:0000766!7.95e-32!76;CL:0000839!1.62e-31!70;CL:0000557!2.80e-30!71;CL:0002009!4.01e-27!65;CL:0002057!9.68e-27!42;CL:0002194!3.30e-26!63;CL:0000576!3.30e-26!63;CL:0000040!3.30e-26!63;CL:0000559!3.30e-26!63;CL:0000860!1.17e-23!45;CL:0000738!5.34e-23!140;CL:0002031!3.47e-22!124;CL:0002087!5.88e-19!119;CL:0002393!9.81e-08!9;CL:0002397!9.81e-08!9
|ontology_enrichment_disease=DOID:8692!1.79e-16!31;DOID:1240!2.67e-13!39;DOID:2531!1.06e-09!51;DOID:0060083!1.06e-09!51
|ontology_enrichment_uberon=UBERON:0002390!6.23e-32!102;UBERON:0003061!6.23e-32!102;UBERON:0002193!6.24e-27!112;UBERON:0002371!7.16e-24!80;UBERON:0001474!4.13e-21!86;UBERON:0002405!7.35e-19!115;UBERON:0003081!6.25e-18!216;UBERON:0004765!2.13e-14!101;UBERON:0001434!2.13e-14!101;UBERON:0000178!2.73e-09!15;UBERON:0000179!2.73e-09!15;UBERON:0000463!2.73e-09!15
}}

Latest revision as of 11:41, 17 September 2013


Full id: C1299_chronic_acute_chorionic_leukemia_choriocarcinoma_pancreatic_placenta



Phase1 CAGE Peaks

Hg19::chr10:11936692..11936705,-p1@ENST00000445498
p1@uc001iky.1
Hg19::chr11:64937702..64937707,+p1@SPDYC
Hg19::chr2:12417696..12417715,-p@chr2:12417696..12417715
-
Hg19::chr2:15696037..15696048,-p@chr2:15696037..15696048
-
Hg19::chr8:129061640..129061667,+p@chr8:129061640..129061667
+
Hg19::chr8:129061678..129061731,+p@chr8:129061678..129061731
+


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:0019901protein kinase binding0.0189420699399505
GO:0019900kinase binding0.0189420699399505
GO:0019899enzyme binding0.0389045880921543



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>disease_data<br>

Cell Type
Ontology termp-valuen
myeloid cell1.46e-23108
common myeloid progenitor1.46e-23108
histamine secreting cell2.45e-215
biogenic amine secreting cell2.45e-215
granulocytopoietic cell2.45e-215
mast cell2.45e-215
mast cell progenitor2.45e-215
basophil mast progenitor cell2.45e-215
hematopoietic stem cell8.44e-18168
angioblastic mesenchymal cell8.44e-18168
hematopoietic cell1.62e-16177
hematopoietic oligopotent progenitor cell7.46e-15161
hematopoietic multipotent progenitor cell7.46e-15161
single nucleate cell1.41e-123
mononuclear cell1.41e-123
endocrine cell1.01e-119
erythroid lineage cell3.12e-092
erythroblast3.12e-092
megakaryocyte-erythroid progenitor cell3.12e-092
erythroid progenitor cell3.12e-092
reticulocyte3.12e-092
proerythroblast3.12e-092
basophilic erythroblast3.12e-092
polychromatophilic erythroblast3.12e-092
orthochromatic erythroblast3.12e-092
Uber Anatomy
Ontology termp-valuen
blood2.26e-1215
haemolymphatic fluid2.26e-1215
organism substance2.26e-1215
Disease
Ontology termp-valuen
myeloid leukemia4.30e-3631
leukemia3.15e-3139
chronic leukemia3.05e-268
hematologic cancer8.18e-2351
immune system cancer8.18e-2351


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)
MA0003.10.0799681
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.85223
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.213007
MA0056.10
MA0057.10.450439
MA0058.11.16137
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.11.51422
MA0072.11.00572
MA0073.10.216116
MA0074.10.660398
MA0076.12.07987
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.419295
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.11.15452
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.12.32339
MA0146.10.232472
MA0147.10.87383
MA0148.10.584698
MA0149.12.52795
MA0062.21.22729
MA0035.21.50688
MA0039.20.200862
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.332548
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.10.508943
MA0164.11.74929
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.476723
MA0102.21.58513
MA0258.10.788656
MA0259.10.893594
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
CCNT2#90555.280167980802190.0005100943974832530.00446627672524761
FOS#235345.998636872596270.001899823711886350.0111814983739475
FOSL1#8061319.85678985818650.0003014027572522190.00310987972383565
GATA1#262336.780154071900220.006765763983348560.0287426628968817
GATA2#262436.3724658667770.008058821308742550.0318808802524153
GTF2B#2959210.64794331144140.01351345865760110.0477220568317173
JUN#372536.256414596168170.008486346850954870.0324036845118045
MAX#414944.301703672671410.006644923910676370.0282902942524613
POLR2A#543062.147453176558070.01019570676818780.037979435002417
REST#597846.433352477418680.001454954223032070.00932347307026914
STAT2#6773332.63188559322036.94270331437341e-050.00110095504319746
TAF1#687252.785871904787740.01078636340290410.0397823571506832
TAL1#6886314.93430833872010.0006952184405921510.00559771171975974
TBP#690853.088975572580320.006645448275786930.0282775412514224
THAP1#55145210.45638153428380.01399147851103650.0491145477350815



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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