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Coexpression cluster:C1407: Difference between revisions

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|tf_chipseq_enrich=CHD2#1106;4:6.89601522274457:0.00111539132013599:0.00766131891375749!IRF3#3661;2:15.6606507371632:0.00641762098993253:0.0279154485034387!MXI1#4601;4:6.6410477525062:0.00128851695803914:0.00863855582107135!PBX3#5090;3:10.9572563433721:0.00171175344181094:0.010689017501303!RFX5#5993;3:6.02395541359755:0.00943790403633506:0.0356035853224055!SIX5#147912;3:8.5433576777295:0.00350475948801243:0.0177979955347919!SMARCC1#6599;3:21.8316796598157:0.000227953389317106:0.00251502472289132!SP1#6667;4:3.7989209187606:0.0105224661679851:0.0389465869553174!TBP#6908;6:3.70677068709639:0.00038541647290796:0.00377745035792365!TCF7L2#6934;3:5.38508828156867:0.0129048877993104:0.0464061418197905!TFAP2C#7022;3:5.40461430493011:0.0127757616669587:0.0460607488516813
|tf_chipseq_enrich=CHD2#1106;4:6.89601522274457:0.00111539132013599:0.00766131891375749!IRF3#3661;2:15.6606507371632:0.00641762098993253:0.0279154485034387!MXI1#4601;4:6.6410477525062:0.00128851695803914:0.00863855582107135!PBX3#5090;3:10.9572563433721:0.00171175344181094:0.010689017501303!RFX5#5993;3:6.02395541359755:0.00943790403633506:0.0356035853224055!SIX5#147912;3:8.5433576777295:0.00350475948801243:0.0177979955347919!SMARCC1#6599;3:21.8316796598157:0.000227953389317106:0.00251502472289132!SP1#6667;4:3.7989209187606:0.0105224661679851:0.0389465869553174!TBP#6908;6:3.70677068709639:0.00038541647290796:0.00377745035792365!TCF7L2#6934;3:5.38508828156867:0.0129048877993104:0.0464061418197905!TFAP2C#7022;3:5.40461430493011:0.0127757616669587:0.0460607488516813
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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.946942,0.436508,0.58616,0.393082,0.584466,0.662701,0.742622,0.267027,0.262261,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.664996,0.402028,0.436569,1.03374,0.576478,0.387783,0.483957,0.730467,0.585619,0.574247,0.396295,0.547818,0.530785,0.92701,0.816912,0.640661,0.35719,0.316592,0.35388,0.585658,0.878269,0.248856,0.355745,0.513952,0.0979105,0.390088,0.354447,0.468392,0.66382,0.542147,0.630853,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,1.57403,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.882224,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.181326,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,1.13818,0.978783,0.430775,0.563054,1.29401,0.352243,0.210279,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.866571,1.07876,0.53374,1.20639,0.692462,1.35529,0.999497,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.424432,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,1.1583,0.83286,0.683502,0.29379,0.661335,3.95476
}}
}}

Revision as of 14:52, 26 November 2012


Full id: C1407_Basophils_Natural_Eosinophils_CD4_CD8_Mast_CD14



Phase1 CAGE Peaks

Hg19::chr15:66111552..66111563,+p@chr15:66111552..66111563
+
Hg19::chr19:55850581..55850600,-p@chr19:55850581..55850600
-
Hg19::chr1:161136054..161136081,-p@chr1:161136054..161136081
-
Hg19::chr2:232469600..232469641,+p@chr2:232469600..232469641
+
Hg19::chr6:30524800..30524820,+p5@PRR3
Hg19::chr9:129482190..129482227,+p@chr9:129482190..129482227
+


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

No GOStat results

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
leukocyte2.48e-35136
hematopoietic stem cell2.58e-30168
angioblastic mesenchymal cell2.58e-30168
nongranular leukocyte4.85e-28115
hematopoietic lineage restricted progenitor cell8.10e-28120
hematopoietic cell1.26e-27177
hematopoietic oligopotent progenitor cell3.56e-27161
hematopoietic multipotent progenitor cell3.56e-27161
classical monocyte1.13e-2042
CD14-positive, CD16-negative classical monocyte1.13e-2042
myeloid leukocyte1.50e-1872
defensive cell3.04e-1648
phagocyte3.04e-1648
granulocyte monocyte progenitor cell3.04e-1667
macrophage dendritic cell progenitor1.41e-1461
myeloid lineage restricted progenitor cell2.83e-1466
myeloid cell3.50e-14108
common myeloid progenitor3.50e-14108
monopoietic cell1.14e-1359
monocyte1.14e-1359
monoblast1.14e-1359
promonocyte1.14e-1359
lymphocyte5.16e-1353
common lymphoid progenitor5.16e-1353
lymphoid lineage restricted progenitor cell1.21e-1252
nucleate cell1.97e-1255
mesenchymal cell3.54e-07354
intermediate monocyte5.82e-079
CD14-positive, CD16-positive monocyte5.82e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.75e-1998
blood island8.75e-1998
bone element2.51e-1682
hemolymphoid system4.39e-16108
bone marrow4.81e-1576
skeletal element1.55e-1390
immune system1.01e-1293
skeletal system6.13e-11100


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
CHD2#110646.896015222744570.001115391320135990.00766131891375749
IRF3#3661215.66065073716320.006417620989932530.0279154485034387
MXI1#460146.64104775250620.001288516958039140.00863855582107135
PBX3#5090310.95725634337210.001711753441810940.010689017501303
RFX5#599336.023955413597550.009437904036335060.0356035853224055
SIX5#14791238.54335767772950.003504759488012430.0177979955347919
SMARCC1#6599321.83167965981570.0002279533893171060.00251502472289132
SP1#666743.79892091876060.01052246616798510.0389465869553174
TBP#690863.706770687096390.000385416472907960.00377745035792365
TCF7L2#693435.385088281568670.01290488779931040.0464061418197905
TFAP2C#702235.404614304930110.01277576166695870.0460607488516813



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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