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Coexpression cluster:C486: Difference between revisions

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|tf_chipseq_enrich=SPI1#6688;7:3.02264550313995:0.00528452342160744:0.0244749597174838
|tf_chipseq_enrich=SPI1#6688;7:3.02264550313995:0.00528452342160744:0.0244749597174838
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|tfbs_overrepresentation_for_novel_motifs=0.38505,0.946977,0.117015,0.212191,0.643195,0.21101,0.267678,0.154541,0.349778,0.282303,0.189673,0.301621,0.259152,0.258863,1.57751,0.343795,0.450873,0.0660543,0.52649,0.202562,0.373792,0.206387,0.205464,0.630143,0.14499,0.3198,1.01201,0.589279,0.651136,0.61444,0.174693,0.483059,1.14885,0.263718,0.262221,0.679792,0.0741766,0.6081,0.226317,0.132023,0.2603,0.163791,0.243154,0.0919607,0.429714,0.833707,0.74012,0.53703,0.78545,0.651467,0.331306,0.27764,0.991471,0.551494,0.691633,0.261104,1.62192,0.665859,0.613944,0.235655,0.519357,0.270343,0.985086,0.426924,0.284296,1.0283,0.774525,1.12911,0.473932,0.971498,0.155159,1.02248,0.0433928,0.689771,0.0237,0.701812,0.955383,0.412445,0.471083,0.141103,1.24363,0.426001,0.284019,0.361652,0.642096,0.0337108,0.356951,2.08417,0.352635,1.2264,0.863265,0.617268,0.497892,0.201541,0.645099,1.24924,0.521585,0.535841,0.356444,0.309213,0.49381,0.492893,0.530844,1.15092,0.387815,0.186536,0.440324,0.256236,0.14483,0.288337,0.390957,0.528368,1.21021,0.196252,1.91278,0.544005,0.466326,0.173882,0.395564,1.67865,0.682065,0.925065,0.209033,0.795647,0.923346,0.413094,1.33772,0.502315,0.721838,0.219699,0.617901,0.176632,0.73532,3.05451,0.875585,2.48667,0.508946,1.11539,0.83506,1.67608,1.2779,0.799588,0.264127,1.31902,0.389296,0.23014,0.979522,1.51807,0.161595,0.0534036,0.623601,0.0148103,0.618251,0.332338,1.3642,1.0011,0.339339,0.607655,0.145027,0.127152,3.11841,0.601304,0.470393,0.805591,0.402913,0.283401,0.720567,0.266654,1.57488
}}
}}

Revision as of 14:15, 26 November 2012


Full id: C486_acute_Neural_chronic_neuroectodermal_caudate_Astrocyte_myelodysplastic



Phase1 CAGE Peaks

Hg19::chr10:105793289..105793301,-p@chr10:105793289..105793301
-
Hg19::chr10:105793325..105793341,-p@chr10:105793325..105793341
-
Hg19::chr10:105793354..105793360,-p@chr10:105793354..105793360
-
Hg19::chr14:23588242..23588262,-p1@CEBPE
Hg19::chr14:23588275..23588288,-p1@CU690200
Hg19::chr14:23588458..23588473,-p2@CEBPE
Hg19::chr16:1537839..1537851,-p@chr16:1537839..1537851
-
Hg19::chr16:1537876..1537921,+p@chr16:1537876..1537921
+
Hg19::chr17:56359033..56359070,-p@chr17:56359033..56359070
-
Hg19::chr22:50523663..50523686,-p7@MLC1
Hg19::chr22:50523689..50523719,-p5@MLC1
Hg19::chr7:2119411..2119445,-p15@MAD1L1
Hg19::chr8:130559296..130559308,+p@chr8:130559296..130559308
+
Hg19::chr8:130695974..130696000,+p@chr8:130695974..130696000
+
Hg19::chr9:100947946..100947962,-p@chr9:100947946..100947962
-
Hg19::chr9:100947965..100947975,-p@chr9:100947965..100947975
-
Hg19::chr9:127148331..127148341,-p@chr9:127148331..127148341
-
Hg19::chr9:127149681..127149698,-p@chr9:127149681..127149698
-
Hg19::chr9:127149714..127149721,-p@chr9:127149714..127149721
-


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:0000093mitotic telophase0.00551925114800423
GO:0051326telophase0.00551925114800423
GO:0000089mitotic metaphase0.00827838931830998
GO:0051323metaphase0.00827838931830998
GO:0051322anaphase0.0091976688152717
GO:0000090mitotic anaphase0.0091976688152717
GO:0000299integral to membrane of membrane fraction0.0126128318365972
GO:0030225macrophage differentiation0.0151734731405287
GO:0007093mitotic cell cycle checkpoint0.0330872449633977
GO:0002573myeloid leukocyte differentiation0.0330872449633977
GO:0006909phagocytosis0.0410950816486348
GO:0000075cell cycle checkpoint0.0477251694968636
GO:0042089cytokine biosynthetic process0.0477251694968636
GO:0007088regulation of mitosis0.0477251694968636
GO:0042107cytokine metabolic process0.0477251694968636
GO:0009059macromolecule biosynthetic process0.0477251694968636
GO:0030099myeloid cell differentiation0.0477251694968636
GO:0005819spindle0.0477251694968636



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><br>uberon_data<br>disease_data<br>


Disease
Ontology termp-valuen
syndrome4.10e-231
hematopoietic system disease2.90e-122
myeloid leukemia6.57e-1231
leukemia1.52e-0939
hematologic cancer2.24e-0751
immune system cancer2.24e-0751
cardiovascular system disease9.11e-074


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)

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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
SPI1#668873.022645503139950.005284523421607440.0244749597174838



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.