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Coexpression cluster:C2312: 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: C2312_testis_Eosinophils_CD14_Neutrophils_Basophils_immature_cord



Phase1 CAGE Peaks

Hg19::chr14:77292773..77292782,+p1@C14orf166B
Hg19::chr1:155960989..155961011,-p@chr1:155960989..155961011
-
Hg19::chr20:44600983..44600997,-p8@ZNF335
Hg19::chr2:69064331..69064344,-p1@ENST00000415448


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 monocyte4.52e-11842
CD14-positive, CD16-negative classical monocyte4.52e-11842
defensive cell3.72e-10248
phagocyte3.72e-10248
myeloid leukocyte2.23e-8872
macrophage dendritic cell progenitor2.48e-8161
monopoietic cell7.17e-8059
monocyte7.17e-8059
monoblast7.17e-8059
promonocyte7.17e-8059
granulocyte monocyte progenitor cell2.53e-7367
myeloid lineage restricted progenitor cell1.48e-7066
myeloid cell1.06e-58108
common myeloid progenitor1.06e-58108
stuff accumulating cell3.34e-5287
leukocyte1.57e-51136
nongranular leukocyte1.35e-43115
hematopoietic stem cell9.01e-40168
angioblastic mesenchymal cell9.01e-40168
hematopoietic lineage restricted progenitor cell3.34e-39120
hematopoietic oligopotent progenitor cell5.34e-38161
hematopoietic multipotent progenitor cell5.34e-38161
hematopoietic cell3.17e-37177
intermediate monocyte3.13e-189
CD14-positive, CD16-positive monocyte3.13e-189
granulocyte2.31e-168
mesenchymal cell2.35e-13354
connective tissue cell6.85e-13361
blood cell1.03e-1111
basophil1.40e-113
motile cell2.95e-11386
stem cell4.84e-10441
multi fate stem cell2.92e-09427
somatic stem cell5.49e-09433
eosinophil7.29e-092
Uber Anatomy
Ontology termp-valuen
bone marrow1.19e-6376
bone element2.29e-5882
hematopoietic system1.25e-5598
blood island1.25e-5598
immune system3.35e-5393
skeletal element2.09e-5290
hemolymphoid system1.27e-49108
skeletal system2.78e-46100
musculoskeletal system4.49e-24167
lateral plate mesoderm2.99e-23203
mesoderm2.21e-13315
mesoderm-derived structure2.21e-13315
presumptive mesoderm2.21e-13315
connective tissue2.95e-12371


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)
MA0003.10.0938548
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
MA0028.11.35734
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
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.13.51802
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
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.12.01886
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
MA0119.12.44319
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
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.11.78721
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.23.34398
MA0099.21.85039
MA0079.20.00910927
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
ESRRA#21011120.9600785340310.008241662461779040.0324823950279536
JUNB#3726215.30531632991060.006126947148475620.0270957077083183



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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