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Coexpression cluster:C3778: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003081!1.16e-22!203;UBERON:0002371!4.71e-17!76;UBERON:0000926!6.30e-16!315;UBERON:0004120!6.30e-16!315;UBERON:0006603!6.30e-16!315;UBERON:0001474!1.22e-15!82;UBERON:0002390!1.62e-15!98;UBERON:0003061!1.62e-15!98;UBERON:0002405!3.99e-15!93;UBERON:0002193!6.45e-15!108;UBERON:0004765!2.46e-13!90;UBERON:0001434!3.89e-11!100;UBERON:0002384!4.21e-11!371;UBERON:0002204!1.43e-10!167;UBERON:0001637!1.09e-08!42;UBERON:0003509!1.09e-08!42;UBERON:0004572!1.09e-08!42;UBERON:0004872!2.21e-08!83;UBERON:0007500!1.79e-07!59;UBERON:0001981!1.79e-07!59;UBERON:0004537!1.79e-07!59;UBERON:0006965!1.79e-07!59;UBERON:0004573!2.90e-07!33;UBERON:0004571!2.90e-07!33;UBERON:0000055!4.05e-07!68
|ontology_enrichment_uberon=UBERON:0003081!1.16e-22!203;UBERON:0002371!4.71e-17!76;UBERON:0000926!6.30e-16!315;UBERON:0004120!6.30e-16!315;UBERON:0006603!6.30e-16!315;UBERON:0001474!1.22e-15!82;UBERON:0002390!1.62e-15!98;UBERON:0003061!1.62e-15!98;UBERON:0002405!3.99e-15!93;UBERON:0002193!6.45e-15!108;UBERON:0004765!2.46e-13!90;UBERON:0001434!3.89e-11!100;UBERON:0002384!4.21e-11!371;UBERON:0002204!1.43e-10!167;UBERON:0001637!1.09e-08!42;UBERON:0003509!1.09e-08!42;UBERON:0004572!1.09e-08!42;UBERON:0004872!2.21e-08!83;UBERON:0007500!1.79e-07!59;UBERON:0001981!1.79e-07!59;UBERON:0004537!1.79e-07!59;UBERON:0006965!1.79e-07!59;UBERON:0004573!2.90e-07!33;UBERON:0004571!2.90e-07!33;UBERON:0000055!4.05e-07!68
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,1.14835,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,0.63803,1.44641,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408
}}
}}

Revision as of 16:21, 26 November 2012


Full id: C3778_Mast_Hair_CD14_CD4_Smooth_Melanocyte_Cardiac



Phase1 CAGE Peaks

Hg19::chr19:35646436..35646495,+p4@FXYD5
Hg19::chr19:35648310..35648360,+p@chr19:35648310..35648360
+
Hg19::chr19:35651604..35651633,+p@chr19:35651604..35651633
+


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
defensive cell2.21e-2248
phagocyte2.21e-2248
classical monocyte5.87e-2142
CD14-positive, CD16-negative classical monocyte5.87e-2142
myeloid lineage restricted progenitor cell8.21e-1966
myeloid leukocyte1.62e-1872
granulocyte monocyte progenitor cell1.68e-1867
monopoietic cell1.41e-1759
monocyte1.41e-1759
monoblast1.41e-1759
promonocyte1.41e-1759
macrophage dendritic cell progenitor1.24e-1661
hematopoietic lineage restricted progenitor cell2.37e-16120
nongranular leukocyte4.03e-16115
hematopoietic oligopotent progenitor cell5.00e-16161
hematopoietic multipotent progenitor cell5.00e-16161
myeloid cell7.89e-16108
common myeloid progenitor7.89e-16108
hematopoietic stem cell9.58e-16168
angioblastic mesenchymal cell9.58e-16168
leukocyte1.05e-14136
native cell7.71e-14722
hematopoietic cell1.24e-13177
multi fate stem cell2.14e-13427
stem cell2.22e-13441
somatic stem cell4.03e-13433
mesenchymal cell1.84e-12354
somatic cell1.89e-12588
connective tissue cell1.18e-11361
stuff accumulating cell5.81e-1187
animal cell3.02e-10679
eukaryotic cell3.02e-10679
motile cell7.45e-08386
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm1.16e-22203
bone marrow4.71e-1776
mesoderm6.30e-16315
mesoderm-derived structure6.30e-16315
presumptive mesoderm6.30e-16315
bone element1.22e-1582
hematopoietic system1.62e-1598
blood island1.62e-1598
immune system3.99e-1593
hemolymphoid system6.45e-15108
skeletal element2.46e-1390
skeletal system3.89e-11100
connective tissue4.21e-11371
musculoskeletal system1.43e-10167
artery1.09e-0842
arterial blood vessel1.09e-0842
arterial system1.09e-0842
splanchnic layer of lateral plate mesoderm2.21e-0883
epithelial tube open at both ends1.79e-0759
blood vessel1.79e-0759
blood vasculature1.79e-0759
vascular cord1.79e-0759
systemic artery2.90e-0733
systemic arterial system2.90e-0733
vessel4.05e-0768


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)

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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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