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Coexpression cluster:C386: Difference between revisions

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|tf_chipseq_enrich=GATA2#2624;11:5.00693746675335:4.20328319157111e-06:0.000133268577184121!TAL1#6886;12:12.8008357189029:3.62005246867039e-11:4.14101489348814e-09
|tf_chipseq_enrich=GATA2#2624;11:5.00693746675335:4.20328319157111e-06:0.000133268577184121!TAL1#6886;12:12.8008357189029:3.62005246867039e-11:4.14101489348814e-09
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|tfbs_overrepresentation_for_novel_motifs=0.211017,0.0448357,0.202592,1.26901,1.91873,0.386501,0.498842,0.156756,0.308585,0.00389105,0.344403,1.69453,1.17026,0.934804,0.0400491,0.0479151,0.323398,0.10615,0.0397851,0.21308,0.446761,0.00644213,0.755166,0.63172,0.546096,0.209525,0.500746,0.116555,0.160764,0.141569,0.0948604,0.352308,0.395527,0.383842,0.124122,0.113304,0.28961,0.122579,0.248146,0.0464435,0.857068,0.0870096,0.327291,0.0395659,0.0955103,0.0673916,0.50051,0.329669,1.55243,0.367635,0.625545,0.518649,0.0825078,1.06572,0.545525,0.161247,0.670339,0.436764,0.264706,0.43528,0.385258,0.972946,0.153907,0.302097,0.53189,0.276238,0.62433,0.968521,0.34408,0.814438,0.0808966,0.553638,0.00128376,0.543765,0.0317128,0.516786,0.067517,0.289314,1.62159,1.88929,0.672562,0.814665,1.61258,0.0601882,0.49889,0.00305957,0.208833,0.414618,0.237365,1.06421,0.709557,0.475666,0.36573,0.414815,0.0407266,0.450781,0.23525,1.03439,0.240628,0.209001,0.101994,0.948453,0.395756,0.326247,0.738351,0.103543,0.313992,0.476111,0.256507,0.0355368,0.47048,0.39349,0.435037,0.110777,2.69813,1.22035,0.00552252,0.313347,0.274506,0.220726,0.536488,0.235652,0.767302,0.18712,0.767667,0.289886,1.51275,0.369745,0.574137,0.0222545,0.476257,0.0962711,0.586948,0.184959,0.721448,0.233081,3.485,0.11686,0.682384,1.50986,1.115,0.648318,0.952311,1.02807,0.269036,0.838665,0.256873,1.35281,0.604229,0.0184789,0.0256312,0.000197059,0.476584,0.0104798,0.971704,0.843272,1.19934,0.143671,0.546227,0.482919,0.647214,0.460792,0.340895,0.0630598,0.28094,0.53011,0.0160931,0.165719,0.000908368
}}
}}

Revision as of 14:10, 26 November 2012


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)

{{{tfbs_overrepresentation_jaspar}}}



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.