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Coexpression cluster:C4169: Difference between revisions

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{{Coexpression_clusters
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of translational initiation!0.0351318733074296!9689$GO:0006413!translational initiation!0.0351318733074296!9689$GO:0003743!translation initiation factor activity!0.0351318733074296!9689$GO:0022618!protein-RNA complex assembly!0.0351318733074296!9689$GO:0006417!regulation of translation!0.0351318733074296!9689$GO:0031326!regulation of cellular biosynthetic process!0.0351318733074296!9689$GO:0008135!translation factor activity, nucleic acid binding!0.0351318733074296!9689$GO:0009889!regulation of biosynthetic process!0.0351318733074296!9689$GO:0022613!ribonucleoprotein complex biogenesis and 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0162.1;0.455568,MA0163.1;0.387745,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.311277,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4169_Mast_CD14_large_migratory_Synoviocyte_immature_Mammary
|id=C4169
}}

Latest revision as of 12:40, 17 September 2013


Full id: C4169_Mast_CD14_large_migratory_Synoviocyte_immature_Mammary



Phase1 CAGE Peaks

Hg19::chr2:201676600..201676667,+p1@BZW1
Hg19::chr2:201676675..201676692,+p3@BZW1
Hg19::chr3:172144898..172144914,-p1@BZW1P1


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

GO IDGO nameFDR corrected p-value
GO:0006446regulation of translational initiation0.0351318733074296
GO:0006413translational initiation0.0351318733074296
GO:0003743translation initiation factor activity0.0351318733074296
GO:0022618protein-RNA complex assembly0.0351318733074296
GO:0006417regulation of translation0.0351318733074296
GO:0031326regulation of cellular biosynthetic process0.0351318733074296
GO:0008135translation factor activity, nucleic acid binding0.0351318733074296
GO:0009889regulation of biosynthetic process0.0351318733074296
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0354017033635543



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
animal cell2.89e-39679
eukaryotic cell2.89e-39679
native cell2.32e-30722
multi fate stem cell4.08e-28427
somatic stem cell5.06e-28433
somatic cell9.66e-28588
stem cell9.81e-28441
connective tissue cell1.72e-20361
mesenchymal cell4.71e-20354
motile cell2.16e-14386
classical monocyte1.86e-1242
CD14-positive, CD16-negative classical monocyte1.86e-1242
myeloid leukocyte7.74e-1272
defensive cell3.29e-1148
phagocyte3.29e-1148
leukocyte5.73e-10136
granulocyte monocyte progenitor cell1.46e-0967
macrophage dendritic cell progenitor2.52e-0961
myeloid lineage restricted progenitor cell5.86e-0966
fibroblast1.52e-0876
monopoietic cell1.59e-0859
monocyte1.59e-0859
monoblast1.59e-0859
promonocyte1.59e-0859
hematopoietic lineage restricted progenitor cell3.81e-07120
myeloid cell4.52e-07108
common myeloid progenitor4.52e-07108
stuff accumulating cell6.69e-0787
Uber Anatomy
Ontology termp-valuen
connective tissue6.91e-19371
musculoskeletal system1.04e-12167
skeletal system6.01e-11100
mesoderm7.86e-10315
mesoderm-derived structure7.86e-10315
presumptive mesoderm7.86e-10315
skeletal element9.58e-1090
bone marrow1.80e-0876
bone element9.05e-0882
immune system2.17e-0793


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



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
BCL3#602223.03140186915890.002464674760842910.0138562828953907
BRCA1#672213.45615376214920.007119807716084560.0296331884613301
ELK4#2005210.8237877723120.01091284719516480.0402048415484625
GTF2B#2959221.29588662288280.002878180589911410.0155853322253205
SIX5#147912211.3911435703060.009873820081429030.037083281627027
ZBTB33#10009221.10981668665410.002928597060603240.0156401998574525



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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