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Coexpression cluster:C2215: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2215_CD14CD16_CD4_CD8_CD19_CD14_Basophils_Whole
|id=C2215
}}

Latest revision as of 12:01, 17 September 2013


Full id: C2215_CD14CD16_CD4_CD8_CD19_CD14_Basophils_Whole



Phase1 CAGE Peaks

Hg19::chr12:53689319..53689349,+p1@PFDN5
Hg19::chr1:160681597..160681619,-p1@CD48
Hg19::chr6:29691170..29691188,+p2@HLA-F
Hg19::chr6:32811861..32811872,+p1@LOC100507463


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
leukocyte4.01e-58136
nongranular leukocyte1.98e-49115
hematopoietic lineage restricted progenitor cell4.34e-49120
hematopoietic stem cell7.95e-46168
angioblastic mesenchymal cell7.95e-46168
hematopoietic oligopotent progenitor cell1.20e-42161
hematopoietic multipotent progenitor cell1.20e-42161
hematopoietic cell1.86e-41177
myeloid leukocyte5.09e-2972
defensive cell3.23e-2648
phagocyte3.23e-2648
granulocyte monocyte progenitor cell3.13e-2567
macrophage dendritic cell progenitor5.70e-2561
myeloid lineage restricted progenitor cell7.00e-2566
monopoietic cell2.64e-2459
monocyte2.64e-2459
monoblast2.64e-2459
promonocyte2.64e-2459
classical monocyte6.19e-2442
CD14-positive, CD16-negative classical monocyte6.19e-2442
nucleate cell1.80e-2255
lymphocyte1.84e-2253
common lymphoid progenitor1.84e-2253
lymphoid lineage restricted progenitor cell3.61e-2252
myeloid cell6.35e-20108
common myeloid progenitor6.35e-20108
mesenchymal cell5.35e-13354
connective tissue cell1.69e-12361
lymphocyte of B lineage1.02e-1124
pro-B cell1.02e-1124
mature alpha-beta T cell9.06e-1118
alpha-beta T cell9.06e-1118
immature T cell9.06e-1118
mature T cell9.06e-1118
immature alpha-beta T cell9.06e-1118
T cell1.74e-1025
pro-T cell1.74e-1025
stuff accumulating cell1.21e-0987
B cell9.08e-0914
multi fate stem cell7.84e-08427
CD8-positive, alpha-beta T cell1.30e-0711
motile cell1.54e-07386
somatic stem cell7.11e-07433
stem cell8.16e-07441
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.31e-3298
blood island6.31e-3298
hemolymphoid system1.37e-29108
immune system1.68e-2393
bone marrow4.42e-2376
bone element6.78e-1882
skeletal element1.35e-1690
skeletal system1.80e-14100
connective tissue1.42e-11371
lateral plate mesoderm3.33e-10203
adult organism1.22e-07114
blood4.25e-0715
haemolymphatic fluid4.25e-0715
organism substance4.25e-0715


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
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
MA0050.12.80362
MA0051.11.91805
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.11.98521
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.11.32557
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.20.476674
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
NFKB1#479045.488063424193840.001102199566301980.00766855109619694
POU2F2#545236.829593043306890.004860473775203740.0227541808511589
TAF1#687243.343046285745290.008005664898701650.0321429969381632
TBP#690843.706770687096390.005296377814784350.0243602590654099



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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