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Coexpression cluster:C3693: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002390!1.24e-23!98;UBERON:0003061!1.24e-23!98;UBERON:0002193!9.74e-22!108;UBERON:0002371!5.98e-18!76;UBERON:0002405!6.60e-18!93;UBERON:0001474!4.58e-16!82;UBERON:0004765!5.94e-14!90;UBERON:0002384!3.64e-12!371;UBERON:0001434!8.37e-12!100
|ontology_enrichment_uberon=UBERON:0002390!1.24e-23!98;UBERON:0003061!1.24e-23!98;UBERON:0002193!9.74e-22!108;UBERON:0002371!5.98e-18!76;UBERON:0002405!6.60e-18!93;UBERON:0001474!4.58e-16!82;UBERON:0004765!5.94e-14!90;UBERON:0002384!3.64e-12!371;UBERON:0001434!8.37e-12!100
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,1.32383,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,2.69227,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,1.54007,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.265282
}}
}}

Revision as of 16:17, 26 November 2012


Full id: C3693_Eosinophils_immature_CD19_Natural_CD34_CD14_CD4



Phase1 CAGE Peaks

Hg19::chr17:76732134..76732147,+p@chr17:76732134..76732147
+
Hg19::chr21:43934704..43934725,-p@chr21:43934704..43934725
-
Hg19::chr6:32821103..32821110,+p@chr6:32821103..32821110
+


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
leukocyte1.07e-62136
hematopoietic cell2.11e-49177
hematopoietic stem cell1.83e-47168
angioblastic mesenchymal cell1.83e-47168
hematopoietic oligopotent progenitor cell1.92e-41161
hematopoietic multipotent progenitor cell1.92e-41161
hematopoietic lineage restricted progenitor cell1.86e-39120
nongranular leukocyte9.84e-38115
myeloid leukocyte1.47e-2872
classical monocyte5.27e-2442
CD14-positive, CD16-negative classical monocyte5.27e-2442
myeloid cell7.72e-23108
common myeloid progenitor7.72e-23108
granulocyte monocyte progenitor cell2.01e-2167
defensive cell3.64e-2048
phagocyte3.64e-2048
macrophage dendritic cell progenitor4.63e-1961
myeloid lineage restricted progenitor cell3.23e-1866
lymphoid lineage restricted progenitor cell1.01e-1752
lymphocyte2.88e-1753
common lymphoid progenitor2.88e-1753
nucleate cell2.09e-1655
monopoietic cell2.62e-1659
monocyte2.62e-1659
monoblast2.62e-1659
promonocyte2.62e-1659
granulocyte6.75e-158
blood cell1.15e-1311
mesenchymal cell1.53e-13354
circulating cell2.25e-136
dendritic cell3.94e-1310
connective tissue cell5.87e-13361
intermediate monocyte6.57e-139
CD14-positive, CD16-positive monocyte6.57e-139
Langerhans cell1.07e-125
motile cell6.42e-11386
CD4-positive, alpha-beta T cell1.39e-096
conventional dendritic cell2.30e-098
lymphocyte of B lineage3.02e-0924
pro-B cell3.02e-0924
natural killer cell9.23e-093
pro-NK cell9.23e-093
multi fate stem cell1.83e-08427
stuff accumulating cell2.30e-0887
stem cell2.83e-08441
somatic stem cell3.95e-08433
basophil5.43e-083
plasmacytoid dendritic cell1.15e-073
single nucleate cell2.60e-073
mononuclear cell2.60e-073
mature alpha-beta T cell5.07e-0718
alpha-beta T cell5.07e-0718
immature T cell5.07e-0718
mature T cell5.07e-0718
immature alpha-beta T cell5.07e-0718
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.24e-2398
blood island1.24e-2398
hemolymphoid system9.74e-22108
bone marrow5.98e-1876
immune system6.60e-1893
bone element4.58e-1682
skeletal element5.94e-1490
connective tissue3.64e-12371
skeletal system8.37e-12100


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

No analysis results for this cluster

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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