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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 12:00, 17 September 2013


Full id: C2178_acute_CD14_Macrophage_Dendritic_anaplastic_chronic_mesothelioma



Phase1 CAGE Peaks

Hg19::chr12:104995242..104995271,+p8@CHST11
Hg19::chr12:104995275..104995304,+p9@CHST11
Hg19::chr12:104995308..104995320,+p15@CHST11
Hg19::chr14:76071877..76071891,+p3@FLVCR2


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:0047756chondroitin 4-sulfotransferase activity0.00485636911762825
GO:0001537N-acetylgalactosamine 4-O-sulfotransferase activity0.00485636911762825
GO:0030206chondroitin sulfate biosynthetic process0.00485636911762825
GO:0030204chondroitin sulfate metabolic process0.00485636911762825
GO:0050650chondroitin sulfate proteoglycan biosynthetic process0.00485636911762825
GO:0050654chondroitin sulfate proteoglycan metabolic process0.00485636911762825
GO:0006024glycosaminoglycan biosynthetic process0.00755301754465224
GO:0030166proteoglycan biosynthetic process0.00755301754465224
GO:0006023aminoglycan biosynthetic process0.00755301754465224
GO:0006029proteoglycan metabolic process0.0093862161464397
GO:0044272sulfur compound biosynthetic process0.0120176833395542
GO:0030203glycosaminoglycan metabolic process0.0120176833395542
GO:0006022aminoglycan metabolic process0.0120176833395542
GO:0008146sulfotransferase activity0.0120176833395542
GO:0016782transferase activity, transferring sulfur-containing groups0.013371554684495
GO:0006790sulfur metabolic process0.0173822650001481
GO:0016051carbohydrate biosynthetic process0.0262316209486302



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 cell6.22e-3148
phagocyte6.22e-3148
monopoietic cell1.10e-2859
monocyte1.10e-2859
monoblast1.10e-2859
promonocyte1.10e-2859
myeloid lineage restricted progenitor cell7.72e-2866
macrophage dendritic cell progenitor2.14e-2761
myeloid cell2.82e-27108
common myeloid progenitor2.82e-27108
classical monocyte1.55e-2642
CD14-positive, CD16-negative classical monocyte1.55e-2642
granulocyte monocyte progenitor cell5.38e-2467
myeloid leukocyte1.33e-2172
hematopoietic oligopotent progenitor cell2.14e-15161
hematopoietic multipotent progenitor cell2.14e-15161
hematopoietic stem cell3.58e-14168
angioblastic mesenchymal cell3.58e-14168
stuff accumulating cell1.25e-1387
hematopoietic cell9.34e-13177
hematopoietic lineage restricted progenitor cell3.02e-12120
nongranular leukocyte1.65e-11115
leukocyte2.48e-10136
conventional dendritic cell3.17e-078
Uber Anatomy
Ontology termp-valuen
bone marrow6.42e-2076
immune system6.21e-1993
bone element1.04e-1782
hematopoietic system2.93e-1698
blood island2.93e-1698
skeletal element3.05e-1590
hemolymphoid system9.31e-15108
skeletal system1.04e-14100
musculoskeletal system4.99e-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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.11.41335
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.12.52375
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.12.31526
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.13.18358
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.12.72365
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.98562
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
IRF1#365935.727872815172930.008097114790333330.0319923796613181
STAT1#6772315.52994062289940.000434088655175550.00404856090890152
STAT2#6773348.94782838983051.42094046481278e-050.000340214583229211



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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