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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:27, 17 September 2013


Full id: C650_CD19_B_lymphoma_xeroderma_splenic_Burkitt_plasma



Phase1 CAGE Peaks

Hg19::chr10:97055058..97055067,-p@chr10:97055058..97055067
-
Hg19::chr11:60236497..60236513,+p@chr11:60236497..60236513
+
Hg19::chr14:106329470..106329481,-p1@IGHJ6
Hg19::chr17:27065235..27065253,+p@chr17:27065235..27065253
+
Hg19::chr21:45627309..45627320,-p1@ENST00000423967
Hg19::chr3:122295630..122295664,+p@chr3:122295630..122295664
+
Hg19::chr4:38807359..38807364,-p6@TLR1
Hg19::chr5:130545735..130545751,+p@chr5:130545735..130545751
+
Hg19::chr5:14213197..14213223,+p@chr5:14213197..14213223
+
Hg19::chr5:88120151..88120177,-p6@MEF2C
Hg19::chr6:167507611..167507627,-p@chr6:167507611..167507627
-
Hg19::chr8:11351178..11351208,+p10@BLK
Hg19::chr9:37371328..37371339,+p@chr9:37371328..37371339
+


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:0001958endochondral ossification0.0123160677063456
GO:0031325positive regulation of cellular metabolic process0.0123160677063456
GO:0009893positive regulation of metabolic process0.0123160677063456
GO:0045410positive regulation of interleukin-6 biosynthetic process0.0123160677063456
GO:0042535positive regulation of tumor necrosis factor biosynthetic process0.0123160677063456
GO:0001974blood vessel remodeling0.0123160677063456
GO:0042534regulation of tumor necrosis factor biosynthetic process0.0123160677063456
GO:0042533tumor necrosis factor biosynthetic process0.0123160677063456
GO:0002062chondrocyte differentiation0.0123160677063456
GO:0042116macrophage activation0.0123160677063456
GO:0045408regulation of interleukin-6 biosynthetic process0.0124401061933039
GO:0042226interleukin-6 biosynthetic process0.0136829082768297
GO:0032640tumor necrosis factor production0.0136829082768297
GO:0032635interleukin-6 production0.0146593956705327
GO:0001649osteoblast differentiation0.0217227219629222
GO:0048522positive regulation of cellular process0.0217227219629222
GO:0002274myeloid leukocyte activation0.0217227219629222
GO:0048518positive regulation of biological process0.0246979622636769
GO:0051216cartilage development0.0259079593262972
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0266922339851133
GO:0042108positive regulation of cytokine biosynthetic process0.0266922339851133
GO:0045727positive regulation of translation0.0329245666875084
GO:0042035regulation of cytokine biosynthetic process0.0341599596012095
GO:0031328positive regulation of cellular biosynthetic process0.0341599596012095
GO:0042089cytokine biosynthetic process0.0354147101214926
GO:0042107cytokine metabolic process0.0354147101214926
GO:0009891positive regulation of biosynthetic process0.0354147101214926
GO:0051247positive regulation of protein metabolic process0.0400479728323247
GO:0001503ossification0.0400479728323247
GO:0031214biomineral formation0.0400479728323247
GO:0007507heart development0.0409485010238248
GO:0046849bone remodeling0.0409485010238248
GO:0048771tissue remodeling0.043418712488239
GO:0001816cytokine production0.0444347976444298
GO:0045087innate immune response0.0444347976444298



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 lineage2.01e-11724
pro-B cell2.01e-11724
B cell3.53e-7114
lymphocyte1.80e-5553
common lymphoid progenitor1.80e-5553
nucleate cell2.78e-5355
lymphoid lineage restricted progenitor cell9.17e-5252
nongranular leukocyte2.67e-27115
leukocyte2.31e-24136
hematopoietic lineage restricted progenitor cell1.26e-21120
hematopoietic stem cell9.38e-19168
angioblastic mesenchymal cell9.38e-19168
hematopoietic oligopotent progenitor cell4.39e-18161
hematopoietic multipotent progenitor cell4.39e-18161
hematopoietic cell1.54e-17177
mature B cell5.28e-132
pre-B-II cell5.28e-132
transitional stage B cell5.28e-132
small pre-B-II cell5.28e-132
immature B cell5.28e-132
precursor B cell5.85e-093
antibody secreting cell2.09e-071
plasma cell2.09e-071
plasmablast2.09e-071
B-1 B cell2.84e-071
Uber Anatomy
Ontology termp-valuen
spleen1.10e-173
gastrointestinal system mesentery1.10e-173
stomach region1.10e-173
mesentery1.10e-173
gastrointestinal system serosa1.10e-173
mesentery of stomach1.10e-173
gut mesentery1.10e-173
dorsal mesentery1.10e-173
dorsal mesogastrium1.10e-173
peritoneal cavity1.10e-173
spleen primordium1.10e-173
hemopoietic organ7.06e-087
immune organ7.06e-087
vermiform appendix2.67e-071
caecum2.67e-071
midgut2.67e-071
tonsil3.21e-071
mucosa-associated lymphoid tissue3.21e-071
lymphoid tissue3.21e-071
tonsillar ring3.21e-071
lymph node3.41e-071
stomach6.00e-078
food storage organ6.00e-078
Disease
Ontology termp-valuen
lymphoma1.71e-2010
genetic disease1.97e-071
monogenic disease1.97e-071
xeroderma pigmentosum1.97e-071
lymphatic system cancer2.84e-071
lymphosarcoma2.84e-071
anemia3.85e-071
acute leukemia6.20e-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)
MA0003.10.014173
MA0004.10.806989
MA0006.10.976306
MA0007.10.282081
MA0009.10.724811
MA0014.10.0622624
MA0017.10.199401
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.535609
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.10.387473
MA0040.10.648455
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.10.131159
MA0050.11.4276
MA0051.10.383704
MA0052.10.652145
MA0055.10.183899
MA0056.10
MA0057.10.0301256
MA0058.10.625569
MA0059.10.623149
MA0060.10.0892161
MA0061.10.255087
MA0063.10
MA0066.11.00709
MA0067.11.03434
MA0068.10.196125
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.10.695528
MA0073.10.0160649
MA0074.10.383033
MA0076.11.22198
MA0077.10.688123
MA0078.10.473657
MA0081.10.623454
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.0644248
MA0089.10
MA0090.10.243681
MA0091.10.30011
MA0092.10.739628
MA0093.10.985558
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.517741
MA0103.10.489275
MA0105.10.10818
MA0106.10.424592
MA0107.10.385539
MA0108.20.568002
MA0109.10
MA0111.10.708492
MA0113.10.439505
MA0114.10.376635
MA0115.10.959312
MA0116.10.391626
MA0117.10.76111
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.10.50732
MA0140.10.350813
MA0141.10.216821
MA0142.10.541045
MA0143.11.11985
MA0144.10.108694
MA0145.10.194261
MA0146.10.0179216
MA0147.10.397782
MA0148.10.319209
MA0149.10.90664
MA0062.20.246574
MA0035.20.350194
MA0039.20.00699112
MA0138.20.474787
MA0002.20.588143
MA0137.20.186529
MA0104.20.298328
MA0047.20.413608
MA0112.20.180347
MA0065.20.388593
MA0150.10.671641
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.10.257061
MA0155.10.333744
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.10.126752
MA0160.10.332385
MA0161.10
MA0162.10.0446668
MA0163.10.0674828
MA0164.10.450848
MA0080.20.171855
MA0018.20.425847
MA0099.20.356906
MA0079.21.6941e-05
MA0102.21.25596
MA0258.10.335505
MA0259.10.412624
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#53335613.09359466320332.65123192532282e-069.28544637990577e-05
EBF1#187974.795789840460230.0002080000784530330.00242285525245999
IRF4#366258.428658725670820.0001867922617576610.00225948540950989
MEF2A#4205710.09250895134681.58302422844669e-066.02073806972848e-05
NFKB1#4790114.643745974317863.97495193507342e-071.92461754820182e-05
PAX5#507973.591304516788060.001263601492487480.0084829514863984
POLR2A#5430121.982264470668990.0007703649959180760.00604070499351963
POU2F2#545285.603768650918481.62953252116393e-050.00037668602695405
SP1#666773.068359203614330.003260177412074160.0168851806962367
TBP#6908102.851362066997220.0002516234088402830.00271004405443646
TCF12#693886.544286093653185.08413564000193e-060.000156678088553013
WRNIP1#56897216.89537913067320.006046898910078670.0270939154519588



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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