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Coexpression cluster:C2717: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.667809270718246,0.873091841190204,0.823024553486482,0,0,0,0,0,0,0.240993089443994,0.440007690464119,0,0,0,0,0,0.147418325487594,0.0497670456196422,0,0,0,0,0,0.0585869700440155,0,0.0495226021424954,0.0460939396382715,0,0,0,0.0374525115654096,0,0.044019022825629,0,0,0,0,0.0394935469382982,0,0,0,0,0,0.0911335404642495,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.06103375120506,0,0,0.34093031616354,0.293292220841452,0.527463003199645,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.172808179578577,0.302009133431584,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0440407241264263,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.993496707815029,0.0780939441312685,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0581777911051045,0.0438332402897762,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0394544993028877,0,0,0,0.749167526111022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0160978224214165,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0511092291180385,0,0,0,0,0,0,0,0.213796647095231,0,0,0,0,0,0.0133047429825382,0,0,0,0,0,0,0,0,0,0,0,0.0349684140344003,0,0,0,0,0.0755587183854606,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0506823072663195,0,0,0,0,0,0,0,0,0,0,0,0,0.0203856949807491,0.273504120918222,0,0,0,0,0,0.0440634162376439,0,0,0,0,0.0111016828724432,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0391580027375375,0.0499125701957491,0,0,0,0,0,0,0,0.0250015116011063,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.071463750344373,0.0782595311904148,0.142197489505522,0,0.0477194411199613,0,0,0,0.188603282786631,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.406507271203569,0,0,0,0,0,0.016408684016216,0,0,0,0,0,0,0,0,0,0,0,0,0,0.077702540701899,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0311684368993006,0.078746383876539,0,0,0,0,0,0,0,0.237803376549433,0.146415578970277,0.667028063622165,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0158614702248811,0,0,0,0,0,0.0135909688377214,0.0624954014614457,0,0,0,0,0,0.101142237885258,0.0547705142198695,0,0,0,0,0,0,0.0250431515419316,0,0,0,0.818078136055912|full_id=C2717_acute_B_xeroderma_b_splenic_plasma_Dendritic|gostat_on_coexpression_clusters=GO:0047372!acylglycerol 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0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.000248021,MA0102.2;1.75932,MA0258.1;1.07498,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2717_acute_B_xeroderma_b_splenic_plasma_Dendritic
|gostat_on_coexpression_clusters=GO:0047372!acylglycerol lipase activity!0.000824208171435299!11343$GO:0004622!lysophospholipase activity!0.00185446838572942!11343$GO:0004620!phospholipase activity!0.0145266690215472!11343$GO:0016298!lipase activity!0.0145266690215472!11343$GO:0004091!carboxylesterase activity!0.0154126928058401!11343$GO:0006954!inflammatory response!0.019987048157306!11343$GO:0009611!response to wounding!0.0249028611797951!11343$GO:0006952!defense response!0.028984654028808!11343$GO:0009605!response to external stimulus!0.028984654028808!11343$GO:0006629!lipid metabolic process!0.0389850465088896!11343$GO:0016788!hydrolase activity, acting on ester bonds!0.041965932728914!11343$GO:0006950!response to stress!0.041965932728914!11343
|id=C2717
|ontology_enrichment_celltype=CL:0002087!1.05e-29!119;CL:0000738!6.17e-29!140;CL:0000037!1.36e-25!172;CL:0000566!1.36e-25!172;CL:0002031!2.45e-24!124;CL:0000988!1.17e-23!182;CL:0002009!1.35e-23!65;CL:0002194!2.24e-23!63;CL:0000576!2.24e-23!63;CL:0000040!2.24e-23!63;CL:0000559!2.24e-23!63;CL:0002032!6.32e-22!165;CL:0000837!6.32e-22!165;CL:0000557!1.91e-20!71;CL:0000839!1.05e-19!70;CL:0000766!4.04e-17!76;CL:0000763!2.04e-15!112;CL:0000049!2.04e-15!112;CL:0002057!2.97e-15!42;CL:0000860!1.08e-14!45;CL:0000945!3.57e-09!24;CL:0000826!3.57e-09!24;CL:0000451!4.11e-09!10
|ontology_enrichment_disease=DOID:0060058!3.31e-08!10;DOID:2531!5.45e-07!51;DOID:0060083!5.45e-07!51
|ontology_enrichment_uberon=UBERON:0002390!1.84e-20!102;UBERON:0003061!1.84e-20!102;UBERON:0002405!2.38e-19!115;UBERON:0002193!2.57e-19!112;UBERON:0002371!6.49e-19!80;UBERON:0001474!1.81e-17!86;UBERON:0004765!1.40e-13!101;UBERON:0001434!1.40e-13!101;UBERON:0007023!6.36e-12!115;UBERON:0004177!8.09e-07!7
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}}

Latest revision as of 12:11, 17 September 2013


Full id: C2717_acute_B_xeroderma_b_splenic_plasma_Dendritic



Phase1 CAGE Peaks

Hg19::chr3:127454947..127454961,-p16@MGLL
Hg19::chr3:127454965..127454984,-p27@MGLL
Hg19::chr3:174988853..174988868,-p1@NAALADL2-AS2
Hg19::chr7:150130832..150130852,+p2@ENST00000486954


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:0047372acylglycerol lipase activity0.000824208171435299
GO:0004622lysophospholipase activity0.00185446838572942
GO:0004620phospholipase activity0.0145266690215472
GO:0016298lipase activity0.0145266690215472
GO:0004091carboxylesterase activity0.0154126928058401
GO:0006954inflammatory response0.019987048157306
GO:0009611response to wounding0.0249028611797951
GO:0006952defense response0.028984654028808
GO:0009605response to external stimulus0.028984654028808
GO:0006629lipid metabolic process0.0389850465088896
GO:0016788hydrolase activity, acting on ester bonds0.041965932728914
GO:0006950response to stress0.041965932728914



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
leukocyte2.27e-25136
lymphocyte of B lineage1.34e-2224
pro-B cell1.34e-2224
nongranular leukocyte1.08e-20115
dendritic cell4.32e-1910
hematopoietic stem cell8.53e-19168
angioblastic mesenchymal cell8.53e-19168
hematopoietic lineage restricted progenitor cell6.38e-18120
hematopoietic cell2.23e-17177
hematopoietic oligopotent progenitor cell4.75e-16161
hematopoietic multipotent progenitor cell4.75e-16161
conventional dendritic cell3.30e-138
plasmacytoid dendritic cell1.09e-113
lymphocyte1.17e-1153
common lymphoid progenitor1.17e-1153
precursor B cell2.34e-113
nucleate cell4.20e-1155
Langerhans cell4.34e-115
lymphoid lineage restricted progenitor cell3.22e-1052
macrophage dendritic cell progenitor6.77e-1061
monopoietic cell5.58e-0959
monocyte5.58e-0959
monoblast5.58e-0959
promonocyte5.58e-0959
granulocyte monocyte progenitor cell1.05e-0867
mature B cell2.88e-082
pre-B-II cell2.88e-082
transitional stage B cell2.88e-082
small pre-B-II cell2.88e-082
immature B cell2.88e-082
myeloid lineage restricted progenitor cell1.07e-0766
myeloid leukocyte8.37e-0772
Uber Anatomy
Ontology termp-valuen
immune system4.99e-1393
hemopoietic organ3.86e-127
immune organ3.86e-127
hematopoietic system5.02e-1298
blood island5.02e-1298
hemolymphoid system1.35e-11108
spleen1.65e-113
gastrointestinal system mesentery1.65e-113
stomach region1.65e-113
mesentery1.65e-113
gastrointestinal system serosa1.65e-113
mesentery of stomach1.65e-113
gut mesentery1.65e-113
dorsal mesentery1.65e-113
dorsal mesogastrium1.65e-113
peritoneal cavity1.65e-113
spleen primordium1.65e-113
bone marrow2.03e-0876
bone element1.54e-0782
Disease
Ontology termp-valuen
lymphoma2.31e-1210
hematologic cancer3.15e-0751
immune system cancer3.15e-0751


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.12.80362
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.12.62367
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.21.83323
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.11.07498
MA0259.10.471671
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
BATF#10538318.26835134422770.0002681660105721290.00286751202806825
EBF1#187936.679850134926750.005184294118278910.0240576954331703
POU2F2#545236.829593043306890.004860473775203740.0227684691907828
SPI1#668836.153242631392040.006580387113059030.0281094952636416



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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