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Coexpression cluster:C3691: Difference between revisions

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|tf_chipseq_enrich=SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000222152526498347
|tf_chipseq_enrich=SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000222152526498347
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|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,0.641468,0.853988,2.1595,0.494933,0.491742,1.84557,1.91835,0.985163,0.436625,0.925331,0.639839,1.60265,1.17594,0.575162,0.452865,2.2774,1.65118,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,1.45286,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,1.54087,0.151453,1.72524,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,2.06667,0.388177,0.891404,1.25741,2.16722,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,4.3166,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,2.58159,0.960908,0.498519,1.39759,4.62073,1.48681,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,0.553386,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,2.3415,1.99724,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135
}}
}}

Revision as of 16:17, 26 November 2012


Full id: C3691_CD14_Mast_Neutrophils_melanoma_Osteoblast_Renal_CD4



Phase1 CAGE Peaks

Hg19::chr17:76354825..76354843,-p8@SOCS3
Hg19::chr17:76355123..76355166,-p4@SOCS3
Hg19::chr17:76355172..76355183,-p14@SOCS3


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
classical monocyte2.00e-2042
CD14-positive, CD16-negative classical monocyte2.00e-2042
myeloid leukocyte1.20e-1772
defensive cell2.08e-1748
phagocyte2.08e-1748
granulocyte monocyte progenitor cell1.85e-1667
macrophage dendritic cell progenitor1.15e-1561
myeloid lineage restricted progenitor cell6.13e-1566
monopoietic cell1.33e-1459
monocyte1.33e-1459
monoblast1.33e-1459
promonocyte1.33e-1459
leukocyte4.07e-14136
hematopoietic lineage restricted progenitor cell6.11e-12120
nongranular leukocyte1.97e-11115
myeloid cell3.63e-09108
common myeloid progenitor3.63e-09108
hematopoietic cell4.69e-09177
hematopoietic stem cell9.97e-09168
angioblastic mesenchymal cell9.97e-09168
connective tissue cell1.15e-08361
hematopoietic oligopotent progenitor cell5.04e-08161
hematopoietic multipotent progenitor cell5.04e-08161
mesenchymal cell2.98e-07354
stuff accumulating cell3.87e-0787
Uber Anatomy
Ontology termp-valuen
skeletal element4.24e-1590
bone marrow2.58e-1476
bone element3.99e-1482
skeletal system6.69e-14100
immune system1.09e-1393
hematopoietic system1.32e-1298
blood island1.32e-1298
hemolymphoid system1.62e-12108
connective tissue3.00e-08371
musculoskeletal system1.05e-07167


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
SUZ12#23512350.11578091106297.93834897779404e-060.000222152526498347



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.