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

Latest revision as of 11:30, 17 September 2013


Full id: C756_Eosinophils_Natural_CD8_CD14_CD4_Basophils_Neutrophils



Phase1 CAGE Peaks

Hg19::chr14:35343724..35343735,+p7@ENST00000557373
Hg19::chr14:52313589..52313620,-p@chr14:52313589..52313620
-
Hg19::chr16:31086162..31086174,+p@chr16:31086162..31086174
+
Hg19::chr16:88522520..88522537,-p@chr16:88522520..88522537
-
Hg19::chr17:57696541..57696548,-p@chr17:57696541..57696548
-
Hg19::chr19:13958525..13958536,+p@chr19:13958525..13958536
+
Hg19::chr1:198648829..198648838,-p2@ENST00000455475
Hg19::chr1:53099124..53099132,-p@chr1:53099124..53099132
-
Hg19::chr2:208395615..208395626,-p@chr2:208395615..208395626
-
Hg19::chrX:48776819..48776823,-p5@PIM2
Hg19::chrX:70338312..70338315,-p@chrX:70338312..70338315
-


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:0007140male meiosis0.012981278700106
GO:0008637apoptotic mitochondrial changes0.0176174496644295
GO:0051327M phase of meiotic cell cycle0.0235782409042741
GO:0007126meiosis0.0235782409042741
GO:0051321meiotic cell cycle0.0235782409042741
GO:0008632apoptotic program0.0235782409042741
GO:0007005mitochondrion organization and biogenesis0.0235782409042741
GO:0006916anti-apoptosis0.0394074531967503
GO:0043066negative regulation of apoptosis0.0426527728717768
GO:0043069negative regulation of programmed cell death0.0426527728717768



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
leukocyte1.02e-31136
hematopoietic stem cell1.91e-24168
angioblastic mesenchymal cell1.91e-24168
granulocyte4.53e-238
hematopoietic cell7.19e-23177
mature alpha-beta T cell9.95e-2218
alpha-beta T cell9.95e-2218
immature T cell9.95e-2218
mature T cell9.95e-2218
immature alpha-beta T cell9.95e-2218
CD4-positive, alpha-beta T cell3.35e-216
hematopoietic oligopotent progenitor cell1.98e-20161
hematopoietic multipotent progenitor cell1.98e-20161
hematopoietic lineage restricted progenitor cell3.73e-17120
natural killer cell4.71e-173
pro-NK cell4.71e-173
blood cell1.27e-1611
basophil5.69e-163
single nucleate cell1.28e-153
mononuclear cell1.28e-153
T cell3.34e-1525
pro-T cell3.34e-1525
nongranular leukocyte1.08e-14115
lymphoid lineage restricted progenitor cell4.30e-1452
lymphocyte8.94e-1453
common lymphoid progenitor8.94e-1453
nucleate cell3.56e-1355
CD1a-positive Langerhans cell5.00e-112
immature CD1a-positive Langerhans cell5.00e-112
myeloid leukocyte1.05e-1072
histamine secreting cell1.30e-095
biogenic amine secreting cell1.30e-095
granulocytopoietic cell1.30e-095
mast cell1.30e-095
mast cell progenitor1.30e-095
basophil mast progenitor cell1.30e-095
myeloid cell1.91e-08108
common myeloid progenitor1.91e-08108
mesenchymal cell4.20e-08354
circulating cell4.73e-086
neutrophil5.17e-083
connective tissue cell8.12e-08361
CD8-positive, alpha-beta T cell8.52e-0811
naive T cell1.17e-073
motile cell8.27e-07386
Uber Anatomy
Ontology termp-valuen
connective tissue2.00e-07371
hematopoietic system5.33e-0798
blood island5.33e-0798


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)
MA0003.11.62403
MA0004.10.349539
MA0006.10.210781
MA0007.10.885261
MA0009.10.79061
MA0014.10.36818
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.0494179
MA0050.10.897608
MA0051.10.439895
MA0052.10.716602
MA0055.10.480412
MA0056.10
MA0057.12.0411
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.10.6764
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.556338
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.708344
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.248289
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.203171
MA0105.11.43099
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.819774
MA0113.10.498009
MA0114.10.465415
MA0115.11.02805
MA0116.10.935607
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.12.15238
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.862195
MA0145.10.515404
MA0146.10.951488
MA0147.10.488526
MA0148.10.372124
MA0149.11.02604
MA0062.20.320507
MA0035.20.404774
MA0039.20.166893
MA0138.20.534556
MA0002.20.358551
MA0137.20.649788
MA0104.20.378829
MA0047.20.47109
MA0112.21.14277
MA0065.20.839576
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.353037
MA0155.11.09568
MA0156.11.22
MA0157.11.41182
MA0158.10
MA0159.10.948902
MA0160.10.386031
MA0161.10
MA0162.10.519336
MA0163.11.7806
MA0164.10.509774
MA0080.20.611699
MA0018.21.21486
MA0099.20.411824
MA0079.21.73043
MA0102.21.32663
MA0258.10.420151
MA0259.10.168926
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
E2F1#186973.12288404583230.002204247145175520.0127012064879992
EBF1#187954.048394021167730.004592383252421630.0217044037695566
NFKB1#479073.492403997214260.001102075485228660.0076969146450312



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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