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Coexpression cluster:C3875: Difference between revisions

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|tf_chipseq_enrich=ESRRA#2101;1:161.280104712042:0.00618762008021956:0.0273512868141554
|tf_chipseq_enrich=ESRRA#2101;1:161.280104712042:0.00618762008021956:0.0273512868141554
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,1.14835,0.305559,0.69094,1.26332,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,1.00813,0.795576,1.21459,0.534793,0.439574,0.599922,0.843849,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.69206,1.55608,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 16:24, 26 November 2012


Full id: C3875_CD14_Whole_CD14CD16_small_Neutrophils_Macrophage_esophagus



Phase1 CAGE Peaks

Hg19::chr1:154980607..154980631,+p@chr1:154980607..154980631
+
Hg19::chr1:154981054..154981102,+p@chr1:154981054..154981102
+
Hg19::chr2:32490859..32490889,-p2@NLRC4


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
myeloid leukocyte4.78e-5572
monopoietic cell7.65e-5559
monocyte7.65e-5559
monoblast7.65e-5559
promonocyte7.65e-5559
macrophage dendritic cell progenitor2.35e-5261
defensive cell9.59e-5048
phagocyte9.59e-5048
myeloid lineage restricted progenitor cell2.27e-4866
granulocyte monocyte progenitor cell2.48e-4767
classical monocyte1.47e-4242
CD14-positive, CD16-negative classical monocyte1.47e-4242
myeloid cell3.37e-41108
common myeloid progenitor3.37e-41108
leukocyte1.42e-29136
nongranular leukocyte4.21e-29115
hematopoietic stem cell1.05e-26168
angioblastic mesenchymal cell1.05e-26168
hematopoietic oligopotent progenitor cell9.68e-26161
hematopoietic multipotent progenitor cell9.68e-26161
hematopoietic lineage restricted progenitor cell3.10e-24120
hematopoietic cell5.43e-24177
stuff accumulating cell1.20e-2387
intermediate monocyte3.43e-129
CD14-positive, CD16-positive monocyte3.43e-129
macrophage1.88e-086
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.21e-4998
blood island6.21e-4998
hemolymphoid system7.11e-45108
bone marrow3.08e-3976
immune system2.67e-3693
bone element7.50e-3582
skeletal element6.08e-3090
skeletal system5.84e-25100
adult organism6.59e-18114
lateral plate mesoderm3.51e-17203
musculoskeletal system1.82e-09167
blood4.19e-0915
haemolymphatic fluid4.19e-0915
organism substance4.19e-0915
mesoderm7.76e-08315
mesoderm-derived structure7.76e-08315
presumptive mesoderm7.76e-08315
organ5.04e-07503
tissue8.11e-07773


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
ESRRA#21011161.2801047120420.006187620080219560.0273512868141554



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.