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Coexpression cluster:C2353: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 12:03, 17 September 2013


Full id: C2353_Mast_immature_Natural_CD8_CD4_CD14_Basophils



Phase1 CAGE Peaks

Hg19::chr15:86126091..86126118,+p7@AKAP13
Hg19::chr15:86127368..86127397,+p@chr15:86127368..86127397
+
Hg19::chr1:204381318..204381339,+p@chr1:204381318..204381339
+
Hg19::chr9:75747095..75747116,+p@chr9:75747095..75747116
+


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
leukocyte5.26e-46136
classical monocyte7.37e-3942
CD14-positive, CD16-negative classical monocyte7.37e-3942
hematopoietic stem cell1.33e-36168
angioblastic mesenchymal cell1.33e-36168
hematopoietic lineage restricted progenitor cell2.48e-35120
hematopoietic cell2.53e-35177
hematopoietic oligopotent progenitor cell4.13e-32161
hematopoietic multipotent progenitor cell4.13e-32161
nongranular leukocyte4.41e-32115
defensive cell4.75e-3248
phagocyte4.75e-3248
myeloid leukocyte5.15e-3272
granulocyte monocyte progenitor cell6.69e-2967
myeloid lineage restricted progenitor cell1.63e-2766
macrophage dendritic cell progenitor3.40e-2661
myeloid cell2.32e-24108
common myeloid progenitor2.32e-24108
monopoietic cell3.46e-2459
monocyte3.46e-2459
monoblast3.46e-2459
promonocyte3.46e-2459
stuff accumulating cell9.71e-1687
mesenchymal cell9.23e-14354
connective tissue cell6.88e-13361
motile cell6.64e-10386
stem cell5.04e-09441
multi fate stem cell6.25e-09427
intermediate monocyte1.85e-089
CD14-positive, CD16-positive monocyte1.85e-089
somatic stem cell2.13e-08433
CD4-positive, alpha-beta T cell4.79e-086
lymphoid lineage restricted progenitor cell7.99e-0852
mature alpha-beta T cell8.24e-0818
alpha-beta T cell8.24e-0818
immature T cell8.24e-0818
mature T cell8.24e-0818
immature alpha-beta T cell8.24e-0818
nucleate cell1.05e-0755
lymphocyte1.53e-0753
common lymphoid progenitor1.53e-0753
Langerhans cell7.79e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.09e-2598
blood island5.09e-2598
bone marrow6.62e-2576
hemolymphoid system7.57e-25108
bone element8.85e-2482
immune system2.87e-2393
skeletal element3.72e-2090
skeletal system3.63e-18100
connective tissue3.28e-12371
lateral plate mesoderm8.05e-12203


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
MA0017.10.577281
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
MA0041.12.91216
MA0042.12.80052
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.15.1904
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.18.301
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
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
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.13.83423
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.27.00686
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
BATF#10538212.17890089615180.009566758805047810.036014227835504
CEBPB#105135.978360719368610.007153832484726970.0297226841258862
FOS#235336.74846648167080.005032452776317940.0234625389717365
JUN#372539.384621894252250.001918994502030470.0112835191305912
PBX3#5090210.95725634337210.01174530180688030.0428320673001423
POU5F1#5460183.85980036297640.01187154239091560.0432380825026969
SPI1#668836.153242631392040.006580387113059030.0280980027679289



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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