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Coexpression cluster:C1488: Difference between revisions

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|tf_chipseq_enrich=ELF1#1997;6:4.25809795880754:0.000167722477628883:0.00205330768269639!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380513657505277!SRF#6722;3:6.8985891310839:0.0064424516893037:0.0280036297489986!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.00573475660696918
|tf_chipseq_enrich=ELF1#1997;6:4.25809795880754:0.000167722477628883:0.00205330768269639!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380513657505277!SRF#6722;3:6.8985891310839:0.0064424516893037:0.0280036297489986!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.00573475660696918
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|tfbs_overrepresentation_for_novel_motifs=1.97464,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,1.36279,0.707204,0.635275,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.800617,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.585619,1.40695,1.81189,0.547818,0.530785,0.92701,0.816912,0.225641,0.939587,0.316592,0.93226,0.585658,0.329602,0.248856,0.355745,0.513952,0.323162,0.390088,0.0393783,0.468392,0.66382,1.33909,0.0909286,1.02586,0.745008,0.675919,0.891214,1.00488,1.15929,1.57403,0.400834,0.62023,1.04504,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.882224,1.15727,1.17153,0.206105,0.192925,0.84426,0.913168,0.477584,0.676305,2.00082,0.684313,0.272514,1.10535,1.55864,0.398737,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.234532,0.987239,1.82799,0.498077,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,1.21459,0.376529,0.44815,0.978783,1.92937,0.563054,1.29401,0.352243,0.460936,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.866571,1.07876,0.53374,1.20639,0.692462,1.35529,0.999497,1.30187,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.826087,0.8388,1.06652,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,0.484017,1.15112,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.521461
}}
}}

Revision as of 14:55, 26 November 2012


Full id: C1488_CD4_CD19_CD14CD16_CD8_Neutrophils_Basophils_Natural



Phase1 CAGE Peaks

Hg19::chr21:43482969..43482994,+p2@UMODL1
Hg19::chr4:83295323..83295348,+p@chr4:83295323..83295348
+
Hg19::chr5:1386528..1386539,-p2@AK127466
Hg19::chr7:144533055..144533069,-p2@TPK1
Hg19::chr8:132916684..132916697,-p@chr8:132916684..132916697
-
Hg19::chr9:115095363..115095398,+p@chr9:115095363..115095398
+


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:0042357thiamin diphosphate metabolic process0.00144820886924134
GO:0004788thiamin diphosphokinase activity0.00144820886924134
GO:0009229thiamin diphosphate biosynthetic process0.00144820886924134
GO:0042724thiamin and derivative biosynthetic process0.00144820886924134
GO:0006772thiamin metabolic process0.00144820886924134
GO:0042723thiamin and derivative metabolic process0.00201134199617551
GO:0016778diphosphotransferase activity0.00482658131089662
GO:0006767water-soluble vitamin metabolic process0.0192921145785954
GO:0006766vitamin metabolic process0.0230358905860548
GO:0009108coenzyme biosynthetic process0.0469337764260271
GO:0051188cofactor biosynthetic process0.0481194432595581



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
leukocyte6.91e-57136
hematopoietic stem cell1.65e-48168
angioblastic mesenchymal cell1.65e-48168
hematopoietic lineage restricted progenitor cell7.52e-47120
nongranular leukocyte1.26e-46115
hematopoietic cell2.45e-45177
hematopoietic oligopotent progenitor cell2.60e-44161
hematopoietic multipotent progenitor cell2.60e-44161
myeloid leukocyte4.26e-2872
granulocyte monocyte progenitor cell1.57e-2467
macrophage dendritic cell progenitor1.17e-2261
lymphoid lineage restricted progenitor cell1.54e-2252
classical monocyte2.44e-2242
CD14-positive, CD16-negative classical monocyte2.44e-2242
myeloid lineage restricted progenitor cell2.49e-2266
lymphocyte5.03e-2253
common lymphoid progenitor5.03e-2253
monopoietic cell8.84e-2259
monocyte8.84e-2259
monoblast8.84e-2259
promonocyte8.84e-2259
myeloid cell1.50e-21108
common myeloid progenitor1.50e-21108
nucleate cell4.68e-2155
defensive cell1.63e-2048
phagocyte1.63e-2048
mature alpha-beta T cell4.64e-1218
alpha-beta T cell4.64e-1218
immature T cell4.64e-1218
mature T cell4.64e-1218
immature alpha-beta T cell4.64e-1218
T cell9.31e-1225
pro-T cell9.31e-1225
lymphocyte of B lineage3.71e-1024
pro-B cell3.71e-1024
CD8-positive, alpha-beta T cell1.23e-0811
B cell4.63e-0814
intermediate monocyte3.09e-079
CD14-positive, CD16-positive monocyte3.09e-079
mesenchymal cell3.36e-07354
Uber Anatomy
Ontology termp-valuen
hemolymphoid system5.07e-30108
hematopoietic system7.31e-3098
blood island7.31e-3098
immune system8.91e-2593
bone marrow2.71e-2376
bone element4.11e-2082
skeletal element1.53e-1590
skeletal system4.70e-12100
lateral plate mesoderm7.25e-10203
adult organism1.45e-07114


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
ELF1#199764.258097958807540.0001677224776288830.00205330768269639
POLR2A#543062.147453176558070.01019570676818780.0380513657505277
SRF#672236.89858913108390.00644245168930370.0280036297489986
TAF1#687263.343046285745290.0007162474284635620.00573475660696918



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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