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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:28, 17 September 2013


Full id: C682_Burkitt_lymphoma_CD19_appendix_tonsil_spleen_diffuse



Phase1 CAGE Peaks

Hg19::chr11:113848216..113848228,+p2@HTR3A
Hg19::chr11:64900812..64900834,-p5@SYVN1
Hg19::chr12:27977018..27977041,-p@chr12:27977018..27977041
-
Hg19::chr12:32418225..32418236,+p@chr12:32418225..32418236
+
Hg19::chr15:89191020..89191067,+p13@ISG20
Hg19::chr1:155953595..155953599,-p@chr1:155953595..155953599
-
Hg19::chr20:43214306..43214347,-p@chr20:43214306..43214347
-
Hg19::chr20:57698461..57698483,+p@chr20:57698461..57698483
+
Hg19::chr22:22398325..22398339,-p1@PRAMEL
Hg19::chr2:220142973..220142983,-p26@TUBA4A
Hg19::chr2:65257848..65257867,+p@chr2:65257848..65257867
+
Hg19::chr2:65257873..65257887,+p@chr2:65257873..65257887
+


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:0008310single-stranded DNA specific 3'-5' exodeoxyribonuclease activity0.0101844084028938
GO:0008859exoribonuclease II activity0.0101844084028938
GO:0005232serotonin-activated cation-selective channel activity0.0101844084028938
GO:0008297single-stranded DNA specific exodeoxyribonuclease activity0.0101844084028938
GO:00082963'-5'-exodeoxyribonuclease activity0.0122207504459862
GO:0000738DNA catabolic process, exonucleolytic0.0135780120329791
GO:0016895exodeoxyribonuclease activity, producing 5'-phosphomonoesters0.0187936840949419
GO:0004529exodeoxyribonuclease activity0.0187936840949419
GO:0043285biopolymer catabolic process0.0187936840949419
GO:0030433ER-associated protein catabolic process0.0187936840949419
GO:0006515misfolded or incompletely synthesized protein catabolic process0.0187936840949419
GO:0044265cellular macromolecule catabolic process0.0187936840949419
GO:00001753'-5'-exoribonuclease activity0.0187936840949419
GO:0004993serotonin receptor activity0.0189047164366943
GO:0016896exoribonuclease activity, producing 5'-phosphomonoesters0.019014415156573
GO:0004532exoribonuclease activity0.019014415156573
GO:0016605PML body0.019014415156573
GO:0009057macromolecule catabolic process0.019014415156573
GO:0016796exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.0234024274421159
GO:0043161proteasomal ubiquitin-dependent protein catabolic process0.0234024274421159
GO:00084083'-5' exonuclease activity0.0258852662218033
GO:0044248cellular catabolic process0.0258852662218033
GO:0006308DNA catabolic process0.0309508886207327
GO:0009056catabolic process0.0341070749707598
GO:0006401RNA catabolic process0.0374058692672204
GO:0004536deoxyribonuclease activity0.0390878569504989
GO:0044446intracellular organelle part0.0403333517367145
GO:0044422organelle part0.0403333517367145
GO:0008227amine receptor activity0.0469240956780526
GO:0004527exonuclease activity0.0471621932387917
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0471621932387917



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 lineage2.37e-9324
pro-B cell2.37e-9324
B cell4.93e-6914
lymphocyte2.98e-4453
common lymphoid progenitor2.98e-4453
nucleate cell1.76e-4255
lymphoid lineage restricted progenitor cell8.62e-4152
nongranular leukocyte7.05e-24115
leukocyte1.91e-19136
single nucleate cell2.82e-173
mononuclear cell2.82e-173
hematopoietic lineage restricted progenitor cell4.52e-15120
hematopoietic stem cell8.30e-15168
angioblastic mesenchymal cell8.30e-15168
hematopoietic cell8.36e-14177
mature B cell2.57e-122
pre-B-II cell2.57e-122
transitional stage B cell2.57e-122
small pre-B-II cell2.57e-122
immature B cell2.57e-122
hematopoietic oligopotent progenitor cell1.89e-11161
hematopoietic multipotent progenitor cell1.89e-11161
circulating cell6.67e-096
precursor B cell1.68e-083
B-1 B cell4.06e-071
antibody secreting cell7.29e-071
plasma cell7.29e-071
plasmablast7.29e-071
Uber Anatomy
Ontology termp-valuen
blood4.29e-0915
haemolymphatic fluid4.29e-0915
organism substance4.29e-0915
spleen1.44e-083
gastrointestinal system mesentery1.44e-083
stomach region1.44e-083
mesentery1.44e-083
gastrointestinal system serosa1.44e-083
mesentery of stomach1.44e-083
gut mesentery1.44e-083
dorsal mesentery1.44e-083
dorsal mesogastrium1.44e-083
peritoneal cavity1.44e-083
spleen primordium1.44e-083
vermiform appendix2.52e-071
caecum2.52e-071
midgut2.52e-071
tonsil3.01e-071
mucosa-associated lymphoid tissue3.01e-071
lymphoid tissue3.01e-071
tonsillar ring3.01e-071
lymph node4.85e-071
Disease
Ontology termp-valuen
lymphoma8.76e-1010
acute leukemia3.82e-071
lymphatic system cancer4.06e-071
lymphosarcoma4.06e-071
genetic disease5.45e-071
monogenic disease5.45e-071
xeroderma pigmentosum5.45e-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)
MA0003.10.00251029
MA0004.10.32225
MA0006.10.188769
MA0007.10.305951
MA0009.10.756202
MA0014.10.00141144
MA0017.11.8359
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.11.87299
MA0040.10.67914
MA0041.13.36019
MA0042.12.30218
MA0043.10.756508
MA0046.10.745626
MA0048.10.155795
MA0050.10.311321
MA0051.10.410316
MA0052.11.63439
MA0055.10.107116
MA0056.10
MA0057.10.0373953
MA0058.10.676094
MA0059.10.239727
MA0060.10.103131
MA0061.10.0856761
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.226673
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.00012619
MA0074.11.05467
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.654005
MA0089.10
MA0090.10.734839
MA0091.10.86696
MA0092.10.291716
MA0093.10.558691
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.11.02503
MA0105.10.130274
MA0106.10.452066
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.761158
MA0113.10.467266
MA0114.10.828144
MA0115.10.992167
MA0116.10.140463
MA0117.10.792789
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.268952
MA0140.10.376643
MA0141.10.670251
MA0142.12.392
MA0143.11.17969
MA0144.10.124153
MA0145.10.232227
MA0146.10.00710499
MA0147.10.143012
MA0148.10.344198
MA0149.10.367947
MA0062.20.0823902
MA0035.20.376007
MA0039.27.40554e-05
MA0138.20.503176
MA0002.20.316618
MA0137.20.20663
MA0104.20.68621
MA0047.20.440861
MA0112.20.0192555
MA0065.20.733267
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.5526
MA0155.10.0793743
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.143477
MA0160.10.357736
MA0161.10
MA0162.10.0188054
MA0163.10.0909552
MA0164.10.478818
MA0080.21.06373
MA0018.20.453345
MA0099.20.382887
MA0079.21.02222e-06
MA0102.21.28978
MA0258.10.117513
MA0259.10.149181
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

No analysis results for this cluster

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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