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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:44, 17 September 2013


Full id: C1413_Mast_immature_CD14_Dendritic_Basophils_CD8_Natural



Phase1 CAGE Peaks

Hg19::chr15:86124958..86125013,+p9@AKAP13
Hg19::chr15:86125966..86125977,+p53@AKAP13
Hg19::chr15:86125992..86126003,+p36@AKAP13
Hg19::chr6:132455044..132455047,-p@chr6:132455044..132455047
-
Hg19::chr6:138115750..138115757,-p@chr6:138115750..138115757
-
Hg19::chr7:28725501..28725529,+p14@CREB5


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:0004691cAMP-dependent protein kinase activity0.0271944660842256
GO:0004690cyclic nucleotide-dependent protein kinase activity0.0271944660842256



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
leukocyte1.46e-42136
hematopoietic stem cell8.54e-33168
angioblastic mesenchymal cell8.54e-33168
hematopoietic cell1.59e-31177
myeloid leukocyte7.78e-3172
hematopoietic oligopotent progenitor cell6.90e-28161
hematopoietic multipotent progenitor cell6.90e-28161
granulocyte monocyte progenitor cell2.19e-2567
hematopoietic lineage restricted progenitor cell2.38e-25120
myeloid cell5.10e-24108
common myeloid progenitor5.10e-24108
nongranular leukocyte1.11e-20115
myeloid lineage restricted progenitor cell3.34e-2066
classical monocyte7.03e-2042
CD14-positive, CD16-negative classical monocyte7.03e-2042
defensive cell2.79e-1848
phagocyte2.79e-1848
macrophage dendritic cell progenitor2.03e-1761
monopoietic cell7.49e-1559
monocyte7.49e-1559
monoblast7.49e-1559
promonocyte7.49e-1559
granulocyte1.34e-148
histamine secreting cell6.94e-125
biogenic amine secreting cell6.94e-125
granulocytopoietic cell6.94e-125
mast cell6.94e-125
mast cell progenitor6.94e-125
basophil mast progenitor cell6.94e-125
blood cell3.09e-1011
stuff accumulating cell5.18e-1087
dendritic cell1.27e-0910
mesenchymal cell5.59e-09354
connective tissue cell1.63e-08361
basophil5.18e-083
plasmacytoid dendritic cell7.45e-083
natural killer cell9.12e-083
pro-NK cell9.12e-083
Langerhans cell9.85e-085
motile cell6.60e-07386
single nucleate cell7.60e-073
mononuclear cell7.60e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.85e-2298
blood island6.85e-2298
bone marrow2.69e-2176
hemolymphoid system4.45e-20108
immune system2.02e-1993
bone element4.48e-1982
skeletal element1.38e-1690
skeletal system4.75e-14100
connective tissue6.92e-08371
lateral plate mesoderm3.80e-07203


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)
MA0003.10.026277
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
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
MA0041.14.75557
MA0042.12.30818
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.737586
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.11.09642
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
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
MA0062.20.658749
MA0035.20.621793
MA0039.20.00570825
MA0138.21.80506
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.0961854
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.10.113377
MA0164.10.738243
MA0080.21.80563
MA0018.20.709805
MA0099.20.629739
MA0079.20.00575781
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
FOS#235345.998636872596270.001899823711886350.0111833890567973
GATA1#262336.780154071900220.006765763983348560.0287508493574049
GATA2#262448.496621155702660.0004993024497617180.00440986457088068
JUN#372536.256414596168170.008486346850954870.0324119794758411



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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