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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:21, 17 September 2013


Full id: C386_chronic_acute_Hodgkin_NK_thymus_liver_blood



Phase1 CAGE Peaks

Hg19::chr11:6423953..6423960,-p19@APBB1
Hg19::chr13:113819053..113819062,+p@chr13:113819053..113819062
+
Hg19::chr13:49070828..49070853,-p@chr13:49070828..49070853
-
Hg19::chr14:23588816..23588836,-p4@CEBPE
Hg19::chr15:58306192..58306225,-p7@ALDH1A2
Hg19::chr15:58306277..58306282,-p41@ALDH1A2
Hg19::chr15:58306295..58306302,-p30@ALDH1A2
Hg19::chr16:89165058..89165067,+p8@ACSF3
Hg19::chr19:7733929..7733950,+p1@RETN
Hg19::chr19:7733964..7733984,+p2@RETN
Hg19::chr1:198988091..198988097,-p@chr1:198988091..198988097
-
Hg19::chr1:54751075..54751101,+p1@ENST00000426901
p1@uc001cxi.1
Hg19::chr2:238933920..238933935,+p7@UBE2F
Hg19::chr2:238933960..238933968,+p9@UBE2F
Hg19::chr4:108984808..108984820,-p@chr4:108984808..108984820
-
Hg19::chr4:145568170..145568180,-p@chr4:145568170..145568180
-
Hg19::chr4:145568348..145568363,-p@chr4:145568348..145568363
-
Hg19::chr4:145568421..145568432,-p@chr4:145568421..145568432
-
Hg19::chr4:145580790..145580817,+p@chr4:145580790..145580817
+
Hg19::chr6:26251989..26252003,+p3@HIST1H2BH
Hg19::chr6:27841151..27841161,-p1@AB451459
Hg19::chrX:123480125..123480142,+p5@SH2D1A
Hg19::chrX:123480155..123480178,+p7@SH2D1A
Hg19::chrX:123480179..123480190,+p9@SH2D1A
Hg19::chrX:123480196..123480210,+p8@SH2D1A
Hg19::chrX:123480214..123480227,+p6@SH2D1A
Hg19::chrX:153200709..153200718,-p5@NAA10
Hg19::chrX:78618558..78618574,-p@chrX:78618558..78618574
-


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:0050760negative regulation of thymidylate synthase biosynthetic process0.0147572510695082
GO:0050758regulation of thymidylate synthase biosynthetic process0.0147572510695082
GO:0050757thymidylate synthase biosynthetic process0.0147572510695082
GO:0001758retinal dehydrogenase activity0.0331969733939237
GO:00040283-chloroallyl aldehyde dehydrogenase activity0.0493885243935911
GO:0045749negative regulation of S phase of mitotic cell cycle0.0493885243935911
GO:0001540beta-amyloid binding0.0493885243935911
GO:0030225macrophage differentiation0.0493885243935911
GO:0007090regulation of S phase of mitotic cell cycle0.0493885243935911
GO:0045930negative regulation of progression through mitotic cell cycle0.0493885243935911
GO:0033261regulation of progression through S phase0.0493885243935911
GO:0006776vitamin A metabolic process0.0493885243935911
GO:0000084S phase of mitotic cell cycle0.0493885243935911
GO:0051246regulation of protein metabolic process0.0493885243935911
GO:0006775fat-soluble vitamin metabolic process0.0493885243935911
GO:0030426growth cone0.0493885243935911
GO:0030427site of polarized growth0.0493885243935911



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
T cell5.28e-1125
pro-T cell5.28e-1125
Uber Anatomy
Ontology termp-valuen
thymus4.21e-294
hemolymphoid system gland4.21e-294
thymic region4.21e-294
pharyngeal gland4.21e-294
thymus primordium4.21e-294
pharyngeal epithelium8.63e-206
hemopoietic organ4.02e-177
immune organ4.02e-177
neck2.66e-1210
gland of gut2.66e-1210
chordate pharynx2.66e-1210
pharyngeal region of foregut2.66e-1210
pharynx2.83e-1111
entire pharyngeal arch endoderm2.83e-1111
early pharyngeal endoderm2.83e-1111
pharyngeal arch system2.95e-0718
upper respiratory tract6.38e-0719
Disease
Ontology termp-valuen
hematologic cancer2.03e-0951
immune system cancer2.03e-0951
leukemia2.73e-0739


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)
MA0003.10.00239715
MA0004.11.17566
MA0006.10.0399016
MA0007.10.0989131
MA0009.10.441048
MA0014.10.0668357
MA0017.10.0536635
MA0019.11.08938
MA0024.10.354374
MA0025.10.557187
MA0027.11.98963
MA0028.10.172603
MA0029.10.369985
MA0030.10.360703
MA0031.10.309631
MA0038.10.168286
MA0040.11.73762
MA0041.10.11856
MA0042.10.10161
MA0043.10.441316
MA0046.10.431829
MA0048.10.0353166
MA0050.10.683588
MA0051.10.165625
MA0052.10.377904
MA0055.10.12662
MA0056.10
MA0057.10.279644
MA0058.11.78731
MA0059.11.27786
MA0060.10.0570653
MA0061.10.116963
MA0063.10
MA0066.10.168556
MA0067.10.724802
MA0068.10.164827
MA0069.11.92193
MA0070.10.419162
MA0071.10.444039
MA0072.10.415392
MA0073.10.0833305
MA0074.10.165153
MA0076.10.528123
MA0077.10.408948
MA0078.10.655763
MA0081.10.845052
MA0083.10.447432
MA0084.10.901266
MA0087.10.413345
MA0088.10.00889845
MA0089.10
MA0090.10.07671
MA0091.10.355228
MA0092.10.303729
MA0093.11.44069
MA0095.10
MA0098.10
MA0100.11.00728
MA0101.10.0419777
MA0103.10.339407
MA0105.10.0245234
MA0106.10.195103
MA0107.10.0213588
MA0108.20.307261
MA0109.10
MA0111.10.282297
MA0113.10.206168
MA0114.10.0202192
MA0115.10.654355
MA0116.10.0963677
MA0117.10.473208
MA0119.10.0566716
MA0122.10.495633
MA0124.10.616574
MA0125.10.541304
MA0130.10
MA0131.10.245067
MA0132.10
MA0133.10
MA0135.10.466979
MA0136.10.172767
MA0139.10.21732
MA0140.10.865299
MA0141.10.0623757
MA0142.10.285297
MA0143.10.594912
MA0144.10.0783755
MA0145.10.000360429
MA0146.13.48383e-05
MA0147.10.747211
MA0148.10.38682
MA0149.10.137231
MA0062.20.110313
MA0035.21.39214
MA0039.20.0999597
MA0138.20.232954
MA0002.21.8053
MA0137.20.0475444
MA0104.20.3076
MA0047.21.04713
MA0112.20.0298612
MA0065.20.259284
MA0150.10.9306
MA0151.10
MA0152.10.146841
MA0153.10.526421
MA0154.10.227743
MA0155.10.641271
MA0156.10.0483557
MA0157.10.264816
MA0158.10
MA0159.10.74979
MA0160.10.408878
MA0161.10
MA0162.10.0264796
MA0163.18.85397e-05
MA0164.10.214689
MA0080.20.158961
MA0018.20.196028
MA0099.20.450447
MA0079.20.0505852
MA0102.20.936833
MA0258.10.605267
MA0259.10.259637
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
GATA2#2624115.006937466753354.20328319157111e-060.000133268577184121
TAL1#68861212.80083571890293.62005246867039e-114.14101489348814e-09



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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