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Coexpression cluster:C1389: Difference between revisions

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|tf_chipseq_enrich=MEF2A#4205;3:9.37161545482203:0.00268739994710391:0.0148016750910023!NFKB1#4790;4:3.65870894946256:0.0120792728901523:0.0438295932103886!RFX5#5993;3:6.02395541359755:0.00943790403633506:0.0356022993444628!TBP#6908;5:3.08897557258032:0.00664544827578693:0.0282867611866201
|tf_chipseq_enrich=MEF2A#4205;3:9.37161545482203:0.00268739994710391:0.0148016750910023!NFKB1#4790;4:3.65870894946256:0.0120792728901523:0.0438295932103886!RFX5#5993;3:6.02395541359755:0.00943790403633506:0.0356022993444628!TBP#6908;5:3.08897557258032:0.00664544827578693:0.0282867611866201
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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.143275,0.436508,1.43205,0.393082,0.584466,0.662701,0.269608,0.267027,0.075749,0.553339,0.707204,0.635275,0.650887,0.391663,0.415981,0.889639,0.892779,0.236034,0.402028,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.225641,0.35719,0.134746,0.35388,0.585658,0.878269,0.69481,0.355745,0.513952,0.323162,1.01199,0.0393783,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,1.94676,0.86037,0.684313,0.272514,1.10535,0.0481066,4.85059,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,1.55741,1.23175,0.987239,0.776336,0.962826,0.881389,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,1.13818,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,1.32127,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,1.91065,0.611524,0.799467,2.01411,1.27188,0.306342,0.424432,0.0926553,1.07915,0.717973,0.665754,1.48627,1.78411,0.378604,1.21528,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,1.48859
}}
}}

Revision as of 14:51, 26 November 2012


Full id: C1389_immature_CD19_CD14_Basophils_migratory_Natural_CD4



Phase1 CAGE Peaks

Hg19::chr14:105281710..105281738,+p1@AY927492
Hg19::chr6:32636347..32636362,+p@chr6:32636347..32636362
+
Hg19::chr6:32636372..32636386,+p@chr6:32636372..32636386
+
Hg19::chr6:32636402..32636417,+p@chr6:32636402..32636417
+
Hg19::chr7:128786662..128786710,+p@chr7:128786662..128786710
+
Hg19::chr7:129133189..129133195,+p@chr7:129133189..129133195
+


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
leukocyte1.87e-90136
nongranular leukocyte2.15e-77115
hematopoietic lineage restricted progenitor cell1.65e-73120
hematopoietic stem cell1.68e-69168
angioblastic mesenchymal cell1.68e-69168
hematopoietic cell7.52e-67177
hematopoietic oligopotent progenitor cell2.28e-62161
hematopoietic multipotent progenitor cell2.28e-62161
classical monocyte8.89e-6142
CD14-positive, CD16-negative classical monocyte8.89e-6142
defensive cell1.08e-5448
phagocyte1.08e-5448
macrophage dendritic cell progenitor1.17e-5061
granulocyte monocyte progenitor cell1.72e-4767
monopoietic cell1.21e-4659
monocyte1.21e-4659
monoblast1.21e-4659
promonocyte1.21e-4659
myeloid leukocyte1.28e-4572
myeloid lineage restricted progenitor cell7.96e-4366
myeloid cell2.82e-35108
common myeloid progenitor2.82e-35108
stuff accumulating cell3.74e-2587
lymphoid lineage restricted progenitor cell1.61e-2452
lymphocyte6.64e-2453
common lymphoid progenitor6.64e-2453
mesenchymal cell1.90e-23354
nucleate cell9.63e-2355
connective tissue cell1.33e-22361
motile cell1.24e-19386
lymphocyte of B lineage2.70e-1924
pro-B cell2.70e-1924
intermediate monocyte2.20e-169
CD14-positive, CD16-positive monocyte2.20e-169
stem cell2.32e-16441
dendritic cell2.58e-1610
multi fate stem cell5.18e-16427
somatic stem cell1.63e-15433
B cell5.59e-1514
Langerhans cell9.38e-135
conventional dendritic cell1.92e-128
plasmacytoid dendritic cell6.86e-083
basophil7.01e-083
single nucleate cell8.81e-083
mononuclear cell8.81e-083
somatic cell1.25e-07588
natural killer cell2.06e-073
pro-NK cell2.06e-073
Uber Anatomy
Ontology termp-valuen
bone marrow1.88e-4076
hematopoietic system1.33e-3798
blood island1.33e-3798
bone element1.29e-3682
hemolymphoid system1.78e-34108
immune system1.66e-3293
skeletal element2.69e-3290
skeletal system7.10e-28100
connective tissue1.88e-21371
lateral plate mesoderm2.41e-12203
musculoskeletal system3.96e-12167


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
MEF2A#420539.371615454822030.002687399947103910.0148016750910023
NFKB1#479043.658708949462560.01207927289015230.0438295932103886
RFX5#599336.023955413597550.009437904036335060.0356022993444628
TBP#690853.088975572580320.006645448275786930.0282867611866201



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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