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{{Coexpression_clusters
{
|full_id=C1612_cord_CD19_Natural_CD8_CD4_CD34_CD14
 

Latest revision as of 11:48, 17 September 2013


Full id: C1612_cord_CD19_Natural_CD8_CD4_CD34_CD14



Phase1 CAGE Peaks

Hg19::chr11:118661169..118661182,+p@chr11:118661169..118661182
+
Hg19::chr12:48499252..48499282,+p7@PFKM
Hg19::chr13:52026730..52026775,-p3@INTS6
Hg19::chr13:52026782..52026796,-p8@INTS6
Hg19::chr6:91005071..91005091,+p@chr6:91005071..91005091
+


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:0006110regulation of glycolysis0.0164013210285011
GO:0016073snRNA metabolic process0.0164013210285011
GO:0016180snRNA processing0.0164013210285011
GO:0032039integrator complex0.0164013210285011
GO:00059456-phosphofructokinase complex0.0164013210285011
GO:00038726-phosphofructokinase activity0.0164013210285011
GO:0009894regulation of catabolic process0.0181253739246214
GO:0008443phosphofructokinase activity0.0181253739246214
GO:0005977glycogen metabolic process0.0248503354425738
GO:0006073glucan metabolic process0.0248503354425738
GO:0006112energy reserve metabolic process0.0254502126700536
GO:0019200carbohydrate kinase activity0.0254502126700536
GO:0008022protein C-terminus binding0.0294586637349271
GO:0044264cellular polysaccharide metabolic process0.0296657322669193
GO:0005976polysaccharide metabolic process0.0296657322669193
GO:0016591DNA-directed RNA polymerase II, holoenzyme0.0350587479266175
GO:0015980energy derivation by oxidation of organic compounds0.0350587479266175
GO:0043234protein complex0.0350587479266175
GO:0006096glycolysis0.0350587479266175
GO:0006007glucose catabolic process0.0350587479266175
GO:0019320hexose catabolic process0.0350587479266175
GO:0046365monosaccharide catabolic process0.0350587479266175
GO:0046164alcohol catabolic process0.0350587479266175
GO:0044275cellular carbohydrate catabolic process0.0367372293616739
GO:0044445cytosolic part0.0367372293616739
GO:0016052carbohydrate catabolic process0.0367372293616739
GO:0006006glucose metabolic process0.0367372293616739
GO:0032991macromolecular complex0.0410504682800081
GO:0019318hexose metabolic process0.047127271035689
GO:0005996monosaccharide metabolic process0.047127271035689



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
leukocyte1.56e-48136
lymphocyte1.53e-4553
common lymphoid progenitor1.53e-4553
lymphoid lineage restricted progenitor cell1.73e-4452
nucleate cell2.51e-4355
hematopoietic cell3.75e-38177
hematopoietic stem cell4.75e-37168
angioblastic mesenchymal cell4.75e-37168
hematopoietic lineage restricted progenitor cell3.08e-33120
nongranular leukocyte1.50e-32115
hematopoietic oligopotent progenitor cell1.49e-31161
hematopoietic multipotent progenitor cell1.49e-31161
lymphocyte of B lineage1.77e-3024
pro-B cell1.77e-3024
B cell7.85e-1814
mature alpha-beta T cell1.26e-1418
alpha-beta T cell1.26e-1418
immature T cell1.26e-1418
mature T cell1.26e-1418
immature alpha-beta T cell1.26e-1418
T cell1.47e-1225
pro-T cell1.47e-1225
circulating cell1.13e-106
CD8-positive, alpha-beta T cell2.94e-1011
dendritic cell6.77e-1010
mesenchymal cell1.23e-08354
connective tissue cell4.39e-08361
Langerhans cell1.18e-075
conventional dendritic cell1.99e-078
CD4-positive, alpha-beta T cell4.21e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.51e-0898
blood island2.51e-0898
hemolymphoid system6.07e-08108
connective tissue9.82e-08371
hemopoietic organ2.63e-077
immune organ2.63e-077
Disease
Ontology termp-valuen
lymphoma1.40e-0810


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)
MA0003.10.737422
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.45664
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.12.31153
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.11.05691
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.16.0382
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.12.08296
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.14.08642
MA0103.10.442769
MA0105.12.26263
MA0106.10.779931
MA0107.14.65287
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.21.12758
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.72541
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.54347
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
BCL3#602213.81884112149530.007902823332280840.0324333136592297
GTF2B#2959212.77753197372970.00919936089559720.0347841154402547
MEF2C#4208216.52454179704960.005579850077982050.0252372769604767
POU2F2#545235.463674434645510.01115650094469780.0409998170999433
RAD21#588548.284027116365060.0004011622639122450.00386467905919481
RDBP#7936261.455361596010.0004178191022410310.00390974009667154
REST#597835.790017229676810.009468788694433940.0356852923808453
SREBF1#6720218.80233977619530.004335312729587370.0205760384533231
TAL1#6886211.94744667097610.0104757781809920.0387985317722126
ZBTB33#10009212.66589001199250.009357016059651590.035336734776856



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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