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

Latest revision as of 11:30, 17 September 2013


Full id: C782_B_Burkitt_lymphoma_splenic_acute_CD19_xeroderma



Phase1 CAGE Peaks

Hg19::chr10:49880649..49880677,+p@chr10:49880649..49880677
+
Hg19::chr12:54446974..54447007,+p@chr12:54446974..54447007
+
Hg19::chr19:39108743..39108750,-p5@MAP4K1
Hg19::chr2:65159543..65159557,-p2@LOC400958
Hg19::chr2:65159562..65159594,-p1@LOC400958
Hg19::chr2:65159616..65159630,-p4@LOC400958
Hg19::chr2:65159651..65159662,-p5@LOC400958
Hg19::chr2:65159748..65159759,-p3@LOC400958
Hg19::chr5:85961934..85961944,+p@chr5:85961934..85961944
+
Hg19::chr6:6587579..6587601,-p3@LY86-AS1


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:0008349MAP kinase kinase kinase kinase activity0.00120687625103026
GO:0045610regulation of hemocyte differentiation0.00120687625103026
GO:0000185activation of MAPKKK activity0.00402292083676753
GO:0042386hemocyte differentiation0.00402292083676753
GO:0018209peptidyl-serine modification0.00402292083676753
GO:0018105peptidyl-serine phosphorylation0.00402292083676753
GO:0007257activation of JNK activity0.00670486806127922
GO:0043507positive regulation of JNK activity0.00670486806127922
GO:0043506regulation of JNK activity0.00670486806127922
GO:0000187activation of MAPK activity0.0120687625103026
GO:0007254JNK cascade0.0120687625103026
GO:0043406positive regulation of MAP kinase activity0.0120687625103026
GO:0031098stress-activated protein kinase signaling pathway0.0120687625103026
GO:0032147activation of protein kinase activity0.0120687625103026
GO:0004702receptor signaling protein serine/threonine kinase activity0.012390596177244
GO:0043405regulation of MAP kinase activity0.0140299364182268
GO:0018193peptidyl-amino acid modification0.0164574034231399
GO:0045860positive regulation of protein kinase activity0.0164574034231399
GO:0045595regulation of cell differentiation0.0164574034231399
GO:0033674positive regulation of kinase activity0.0164574034231399
GO:0051347positive regulation of transferase activity0.0164574034231399
GO:0000165MAPKKK cascade0.0164574034231399
GO:0030097hemopoiesis0.0168962675144236
GO:0048534hemopoietic or lymphoid organ development0.0168962675144236
GO:0005057receptor signaling protein activity0.0168962675144236
GO:0002520immune system development0.0168962675144236
GO:0050793regulation of developmental process0.0198732289336316
GO:0045859regulation of protein kinase activity0.0198732289336316
GO:0043549regulation of kinase activity0.0198732289336316
GO:0051338regulation of transferase activity0.0198732289336316
GO:0043085positive regulation of catalytic activity0.0199329238879836
GO:0007243protein kinase cascade0.0283615918992111
GO:0005083small GTPase regulator activity0.0345971191962008
GO:0050790regulation of catalytic activity0.0429505959925475
GO:0065009regulation of a molecular function0.0456655878768206
GO:0004674protein serine/threonine kinase activity0.0456655878768206
GO:0030695GTPase regulator activity0.0456655878768206



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
lymphocyte of B lineage1.14e-10924
pro-B cell1.14e-10924
B cell3.80e-6114
lymphocyte3.03e-5253
common lymphoid progenitor3.03e-5253
nucleate cell3.50e-5055
lymphoid lineage restricted progenitor cell2.53e-4852
nongranular leukocyte7.25e-26115
hematopoietic lineage restricted progenitor cell2.61e-22120
leukocyte3.72e-21136
hematopoietic oligopotent progenitor cell3.87e-17161
hematopoietic multipotent progenitor cell3.87e-17161
hematopoietic stem cell3.17e-16168
angioblastic mesenchymal cell3.17e-16168
hematopoietic cell3.70e-15177
mature B cell3.18e-132
pre-B-II cell3.18e-132
transitional stage B cell3.18e-132
small pre-B-II cell3.18e-132
immature B cell3.18e-132
precursor B cell4.15e-093
antibody secreting cell1.42e-071
plasma cell1.42e-071
plasmablast1.42e-071
B-1 B cell2.50e-071
Uber Anatomy
Ontology termp-valuen
spleen1.06e-183
gastrointestinal system mesentery1.06e-183
stomach region1.06e-183
mesentery1.06e-183
gastrointestinal system serosa1.06e-183
mesentery of stomach1.06e-183
gut mesentery1.06e-183
dorsal mesentery1.06e-183
dorsal mesogastrium1.06e-183
peritoneal cavity1.06e-183
spleen primordium1.06e-183
hemopoietic organ8.10e-147
immune organ8.10e-147
vermiform appendix2.35e-071
caecum2.35e-071
midgut2.35e-071
stomach2.51e-078
food storage organ2.51e-078
tonsil2.66e-071
mucosa-associated lymphoid tissue2.66e-071
lymphoid tissue2.66e-071
tonsillar ring2.66e-071
Disease
Ontology termp-valuen
lymphoma7.25e-2210
acute leukemia1.10e-071
lymphatic system cancer2.50e-071
lymphosarcoma2.50e-071
genetic disease2.83e-071
monogenic disease2.83e-071
xeroderma pigmentosum2.83e-071
anemia3.62e-071


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)
MA0003.10.0250581
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.0036779
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.965046
MA0051.10.473017
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.10.802927
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.757837
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.000128517
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.0309101
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.11.20737
MA0105.10.422512
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.11.62509
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.353333
MA0140.11.11568
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.14293
MA0146.10.128432
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.366815
MA0035.21.11424
MA0039.20.520808
MA0138.20.569505
MA0002.21.90479
MA0137.20.255808
MA0104.20.138396
MA0047.21.25985
MA0112.20.133417
MA0065.20.615279
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.12.09876
MA0155.10.296882
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.11.04074
MA0160.10.417847
MA0161.10
MA0162.10.0377269
MA0163.10.00405048
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.21.12985
MA0079.20.0513543
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
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
BCL11A#53335617.02167306216423.55593058662976e-071.75592356755095e-05
EBF1#187998.01582016191212.54528393136776e-081.77099872423796e-06
ELF1#199793.832288162926781.71269377095518e-050.000392005313926775
IRF4#3662510.95725634337214.10495409675721e-050.000745724997236435
MEF2A#420535.622969272893220.01372403878188040.0483251816028592
NFKB1#479084.390450739355073.83990628335229e-050.000723630408385114
PAX5#507974.668695871824480.0001341235735206540.00175910233516559
PBX3#5090613.14870761204651.61405405165394e-066.12982513093401e-05
POLR2A#543091.932707858902260.005980089183606110.0268106689953483
POU2F2#545298.195511651968272.08994783441932e-081.48484395836e-06
SP1#666784.558705102512722.88273233272976e-050.000603587975336736
TAF1#687272.34013240002170.01040839844348330.038631178259318
TBP#690882.965416549677110.0007302875668644710.00581640381268653
TCF12#693888.507571921749142.30735866354801e-071.21767676332638e-05
YY1#752862.946702449912310.006987247873951880.0295370023762511
ZEB1#6935711.82190241228072.60652199876196e-071.34696957461009e-05



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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