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Coexpression cluster:C1704: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:5.06896126157011:0.00270999809128077:0.0148931535811025!CHD2#1106;3:6.20641370047011:0.00777455012627559:0.0319483077174148!E2F1#1869;4:3.92591137190346:0.00721498454710636:0.0298721812136865!EGR1#1958;4:3.99054327584811:0.006780098300144:0.0287614413634744!ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447304050252729!GABPB1#2553;4:5.65414706894574:0.00177669650209667:0.0109061012097375!GTF2B#2959;2:12.7775319737297:0.0091993608955972:0.0347866342943363!GTF2F1#2962;4:10.1917287014061:0.00017783388942764:0.00215837229261282!MAX#4149;4:5.1620444072057:0.00252630900948518:0.013996349617613!MEF2C#4208;2:16.5245417970496:0.00557985007798205:0.0252416495124688!MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256743350711239!NFKB1#4790;5:5.48806342419384:0.000200816284746232:0.00238900238781315!POU2F2#5452;4:7.28489924619402:0.000663122328874386:0.00542332285867752!REST#5978;3:5.79001722967681:0.00946878869443394:0.0356930203731317!SP1#6667;4:4.55870510251272:0.0040757356578168:0.019478595907506!SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00714100112477938!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135242071647417!TAF7#6879;3:6.85984164295435:0.00584328640701904:0.0262423990136599!TAL1#6886;2:11.9474466709761:0.010475778180992:0.0388040360859948!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00918093610969343!YY1#7528;4:3.92893659988308:0.00719386626991762:0.0298367896177247
|tf_chipseq_enrich=CCNT2#905;4:5.06896126157011:0.00270999809128077:0.0148931535811025!CHD2#1106;3:6.20641370047011:0.00777455012627559:0.0319483077174148!E2F1#1869;4:3.92591137190346:0.00721498454710636:0.0298721812136865!EGR1#1958;4:3.99054327584811:0.006780098300144:0.0287614413634744!ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447304050252729!GABPB1#2553;4:5.65414706894574:0.00177669650209667:0.0109061012097375!GTF2B#2959;2:12.7775319737297:0.0091993608955972:0.0347866342943363!GTF2F1#2962;4:10.1917287014061:0.00017783388942764:0.00215837229261282!MAX#4149;4:5.1620444072057:0.00252630900948518:0.013996349617613!MEF2C#4208;2:16.5245417970496:0.00557985007798205:0.0252416495124688!MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256743350711239!NFKB1#4790;5:5.48806342419384:0.000200816284746232:0.00238900238781315!POU2F2#5452;4:7.28489924619402:0.000663122328874386:0.00542332285867752!REST#5978;3:5.79001722967681:0.00946878869443394:0.0356930203731317!SP1#6667;4:4.55870510251272:0.0040757356578168:0.019478595907506!SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00714100112477938!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135242071647417!TAF7#6879;3:6.85984164295435:0.00584328640701904:0.0262423990136599!TAL1#6886;2:11.9474466709761:0.010475778180992:0.0388040360859948!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00918093610969343!YY1#7528;4:3.92893659988308:0.00719386626991762:0.0298367896177247
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.787587,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.345702,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.969147,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.94379,0.27659,0.417272,0.432883,1.06371,0.654459,0.388123,0.301779,0.415749,0.580638,0.414516,0.451846,0.476793,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.86107,0.935408,1.78554,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.554326,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.796279,0.934302,0.755403,0.327263,1.18161,0.914416,0.49825,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,1.15465,0.381528,0.28626,1.06255,0.849074,0.606298,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,2.18702,0.717647,0.549347,1.11542,1.27602,1.05402,0.494368,0.631235,1.37132,0.412056,0.597842,1.45429,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,2.85991,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,1.63047,0.87256,2.09294,0.577088,0.953361,1.00998,1.29319,1.15522,0.840171,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,1.65153,0.731946,0.443702
}}
}}

Revision as of 15:03, 26 November 2012


Full id: C1704_CD4_Dendritic_CD8_CD19_Natural_Basophils_Eosinophils



Phase1 CAGE Peaks

Hg19::chr13:28024374..28024401,+p@chr13:28024374..28024401
+
Hg19::chr15:50647015..50647042,-p2@FLJ10038
Hg19::chr2:55845029..55845079,+p@chr2:55845029..55845079
+
Hg19::chr6:42713792..42713847,-p1@TBCC
Hg19::chrX:106960429..106960457,+p@chrX:106960429..106960457
+


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:0007023post-chaperonin tubulin folding pathway0.00147180030613446
GO:0007025beta-tubulin folding0.00183975038266808
GO:0007021tubulin folding0.0022077004592017
GO:0051087chaperone binding0.00294360061226893
GO:0005874microtubule0.0423142588013658
GO:0006457protein folding0.0423142588013658



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><br>


Cell Type
Ontology termp-valuen
hematopoietic cell6.75e-40177
hematopoietic stem cell2.65e-39168
angioblastic mesenchymal cell2.65e-39168
leukocyte8.39e-37136
hematopoietic oligopotent progenitor cell2.41e-35161
hematopoietic multipotent progenitor cell2.41e-35161
hematopoietic lineage restricted progenitor cell1.75e-28120
nongranular leukocyte3.78e-27115
nucleate cell3.61e-1955
lymphocyte1.41e-1853
common lymphoid progenitor1.41e-1853
lymphoid lineage restricted progenitor cell3.12e-1852
myeloid cell8.44e-17108
common myeloid progenitor8.44e-17108
myeloid leukocyte1.56e-1372
mature alpha-beta T cell7.50e-1218
alpha-beta T cell7.50e-1218
immature T cell7.50e-1218
mature T cell7.50e-1218
immature alpha-beta T cell7.50e-1218
granulocyte monocyte progenitor cell4.48e-1167
T cell8.32e-1125
pro-T cell8.32e-1125
myeloid lineage restricted progenitor cell1.60e-1066
macrophage dendritic cell progenitor2.52e-0961
classical monocyte5.64e-0942
CD14-positive, CD16-negative classical monocyte5.64e-0942
monopoietic cell1.22e-0859
monocyte1.22e-0859
monoblast1.22e-0859
promonocyte1.22e-0859
B cell2.39e-0814
CD8-positive, alpha-beta T cell3.67e-0811
connective tissue cell8.91e-08361
mesenchymal cell1.51e-07354
lymphocyte of B lineage3.83e-0724
pro-B cell3.83e-0724
defensive cell4.43e-0748
phagocyte4.43e-0748
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.23e-1698
blood island2.23e-1698
hemolymphoid system2.73e-16108
immune system3.45e-1193
bone marrow8.20e-1076
bone element3.62e-0982
skeletal element8.91e-0890
blood2.16e-0715
haemolymphatic fluid2.16e-0715
organism substance2.16e-0715


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
CCNT2#90545.068961261570110.002709998091280770.0148931535811025
CHD2#110636.206413700470110.007774550126275590.0319483077174148
E2F1#186943.925911371903460.007214984547106360.0298721812136865
EGR1#195843.990543275848110.0067800983001440.0287614413634744
ELF1#199743.406478367046030.01235066105299550.0447304050252729
GABPB1#255345.654147068945740.001776696502096670.0109061012097375
GTF2B#2959212.77753197372970.00919936089559720.0347866342943363
GTF2F1#2962410.19172870140610.000177833889427640.00215837229261282
MAX#414945.16204440720570.002526309009485180.013996349617613
MEF2C#4208216.52454179704960.005579850077982050.0252416495124688
MYC#460944.177825497287520.005691969036823440.0256743350711239
NFKB1#479055.488063424193840.0002008162847462320.00238900238781315
POU2F2#545247.284899246194020.0006631223288743860.00542332285867752
REST#597835.790017229676810.009468788694433940.0356930203731317
SP1#666744.558705102512720.00407573565781680.019478595907506
SPI1#668846.563458806818180.0009957429636454020.00714100112477938
TAF1#687253.343046285745290.002394600090870310.0135242071647417
TAF7#687936.859841642954350.005843286407019040.0262423990136599
TAL1#6886211.94744667097610.0104757781809920.0388040360859948
TBP#690853.706770687096390.001428755106721120.00918093610969343
YY1#752843.928936599883080.007193866269917620.0298367896177247



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.