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Coexpression cluster:C1422: Difference between revisions

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

Latest revision as of 11:44, 17 September 2013


Full id: C1422_mature_CD14_Mast_Eosinophils_immature_heart_Neutrophils



Phase1 CAGE Peaks

Hg19::chr16:56644227..56644239,-p@chr16:56644227..56644239
-
Hg19::chr1:161187227..161187240,+p@chr1:161187227..161187240
+
Hg19::chr3:150126101..150126118,+p6@TSC22D2
Hg19::chr4:139936055..139936069,+p@chr4:139936055..139936069
+
Hg19::chr4:139936290..139936301,+p@chr4:139936290..139936301
+
Hg19::chr6:89745175..89745188,-p@chr6:89745175..89745188
-


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 monocyte5.97e-3242
CD14-positive, CD16-negative classical monocyte5.97e-3242
defensive cell6.46e-2748
phagocyte6.46e-2748
myeloid leukocyte9.00e-2672
granulocyte monocyte progenitor cell2.32e-2467
myeloid lineage restricted progenitor cell3.76e-2366
macrophage dendritic cell progenitor3.25e-2261
monopoietic cell1.67e-2159
monocyte1.67e-2159
monoblast1.67e-2159
promonocyte1.67e-2159
stuff accumulating cell1.57e-1687
leukocyte1.23e-15136
myeloid cell4.25e-15108
common myeloid progenitor4.25e-15108
hematopoietic lineage restricted progenitor cell1.82e-13120
nongranular leukocyte1.33e-12115
hematopoietic stem cell1.23e-10168
angioblastic mesenchymal cell1.23e-10168
hematopoietic cell2.76e-10177
hematopoietic oligopotent progenitor cell5.87e-10161
hematopoietic multipotent progenitor cell5.87e-10161
mesenchymal cell8.27e-09354
connective tissue cell2.38e-08361
natural killer cell6.71e-073
pro-NK cell6.71e-073
motile cell9.18e-07386
Uber Anatomy
Ontology termp-valuen
bone marrow5.88e-2276
bone element3.82e-2182
hematopoietic system6.79e-2098
blood island6.79e-2098
immune system1.10e-1893
skeletal element1.99e-1890
hemolymphoid system2.72e-18108
skeletal system1.17e-15100
lateral plate mesoderm1.08e-10203
connective tissue3.27e-08371
musculoskeletal system3.93e-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)
MA0003.10.00461978
MA0004.11.37419
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.808182
MA0056.10
MA0057.10.450439
MA0058.11.16137
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.80532
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.10.865577
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.200862
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.0146751
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
CEBPB#105145.314098417216540.003008047293917460.0159803373177397
FOSL2#235538.465100302280850.003598315634615090.0182243580119085
GTF2F1#296236.369830438378830.008068208196303160.0319168060230183
JUN#372536.256414596168170.008486346850954870.032413164817396
JUND#372744.663109294580680.004917643408260230.0229909020061458
MAFF#23764218.77178549664840.004508988280519180.0213295691198996
STAT1#6772310.35329374859960.002016680459920930.0117213028300786
STAT3#677447.012976664769490.001045723664135530.00739333426473401
TRIM28#1015539.295262522631260.00275136505059490.015091902023061
ZNF263#1012745.481227758007120.002675609380607230.0147460669182711



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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