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Coexpression cluster:C1612: Difference between revisions

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|tf_chipseq_enrich=BCL3#602;2:13.8188411214953:0.00790282333228084:0.0324333136592297!GTF2B#2959;2:12.7775319737297:0.0091993608955972:0.0347841154402547!MEF2C#4208;2:16.5245417970496:0.00557985007798205:0.0252372769604767!POU2F2#5452;3:5.46367443464551:0.0111565009446978:0.0409998170999433!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386467905919481!RDBP#7936;2:61.45536159601:0.000417819102241031:0.00390974009667154!REST#5978;3:5.79001722967681:0.00946878869443394:0.0356852923808453!SREBF1#6720;2:18.8023397761953:0.00433531272958737:0.0205760384533231!TAL1#6886;2:11.9474466709761:0.010475778180992:0.0387985317722126!ZBTB33#10009;2:12.6658900119925:0.00935701605965159:0.035336734776856
|tf_chipseq_enrich=BCL3#602;2:13.8188411214953:0.00790282333228084:0.0324333136592297!GTF2B#2959;2:12.7775319737297:0.0091993608955972:0.0347841154402547!MEF2C#4208;2:16.5245417970496:0.00557985007798205:0.0252372769604767!POU2F2#5452;3:5.46367443464551:0.0111565009446978:0.0409998170999433!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386467905919481!RDBP#7936;2:61.45536159601:0.000417819102241031:0.00390974009667154!REST#5978;3:5.79001722967681:0.00946878869443394:0.0356852923808453!SREBF1#6720;2:18.8023397761953:0.00433531272958737:0.0205760384533231!TAL1#6886;2:11.9474466709761:0.010475778180992:0.0387985317722126!ZBTB33#10009;2:12.6658900119925:0.00935701605965159:0.035336734776856
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|tfbs_overrepresentation_for_novel_motifs=0.508327,1.20042,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.106358,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.167776,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,0.94379,0.27659,1.0713,1.1597,0.413782,0.654459,0.388123,1.48009,0.415749,0.580638,0.414516,0.451846,0.218848,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.554326,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.963115,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.780629,1.06255,0.849074,1.14173,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.285668,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,1.63047,0.87256,2.09294,0.577088,0.363423,0.177807,0.79475,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,1.2893,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.443702
}}
}}

Revision as of 15:00, 26 November 2012


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)

{{{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
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.