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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 11:29, 17 September 2013


Full id: C719_Neutrophils_CD14CD16_CD14_blood_Eosinophils_Peripheral_Monocytederived



Phase1 CAGE Peaks

Hg19::chr10:134401859..134401869,-p@chr10:134401859..134401869
-
Hg19::chr12:12871211..12871230,-p@chr12:12871211..12871230
-
Hg19::chr15:86098670..86098685,+p26@AKAP13
Hg19::chr17:2303981..2304001,+p@chr17:2303981..2304001
+
Hg19::chr19:10961109..10961114,+p@chr19:10961109..10961114
+
Hg19::chr19:18508474..18508483,-p2@LRRC25
Hg19::chr1:145439323..145439355,+p10@TXNIP
Hg19::chr20:30671781..30671788,+p@chr20:30671781..30671788
+
Hg19::chr3:195627582..195627593,-p@chr3:195627582..195627593
-
Hg19::chr6:31583295..31583313,+p9@AIF1
Hg19::chr7:76825469..76825505,-p@chr7:76825469..76825505
-


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 monocyte5.47e-9842
CD14-positive, CD16-negative classical monocyte5.47e-9842
defensive cell5.81e-9348
phagocyte5.81e-9348
myeloid leukocyte3.62e-8872
macrophage dendritic cell progenitor8.47e-8061
monopoietic cell3.95e-7959
monocyte3.95e-7959
monoblast3.95e-7959
promonocyte3.95e-7959
granulocyte monocyte progenitor cell1.17e-7167
myeloid lineage restricted progenitor cell1.40e-6966
myeloid cell2.17e-59108
common myeloid progenitor2.17e-59108
leukocyte9.32e-53136
stuff accumulating cell5.52e-4687
nongranular leukocyte3.95e-45115
hematopoietic stem cell9.46e-42168
angioblastic mesenchymal cell9.46e-42168
hematopoietic cell6.67e-39177
hematopoietic oligopotent progenitor cell1.30e-38161
hematopoietic multipotent progenitor cell1.30e-38161
hematopoietic lineage restricted progenitor cell1.96e-38120
intermediate monocyte7.21e-269
CD14-positive, CD16-positive monocyte7.21e-269
granulocyte2.82e-178
mesenchymal cell2.30e-12354
blood cell3.11e-1211
connective tissue cell7.40e-12361
non-classical monocyte4.19e-103
CD14-low, CD16-positive monocyte4.19e-103
motile cell4.45e-10386
neutrophil5.14e-103
single nucleate cell3.34e-093
mononuclear cell3.34e-093
basophil5.80e-093
multi fate stem cell6.28e-08427
somatic stem cell1.23e-07433
stem cell2.94e-07441
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.82e-8798
blood island8.82e-8798
hemolymphoid system2.23e-80108
bone marrow7.92e-6276
immune system9.97e-6193
bone element1.84e-5682
skeletal element2.07e-5090
skeletal system3.38e-44100
lateral plate mesoderm6.26e-36203
musculoskeletal system9.36e-22167
blood4.26e-2015
haemolymphatic fluid4.26e-2015
organism substance4.26e-2015
mesoderm7.76e-19315
mesoderm-derived structure7.76e-19315
presumptive mesoderm7.76e-19315
connective tissue3.63e-11371


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)
MA0003.10.226717
MA0004.10.349539
MA0006.10.605586
MA0007.10.332734
MA0009.10.79061
MA0014.10.0481212
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
MA0038.11.12886
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.185335
MA0050.10.338274
MA0051.10.439895
MA0052.11.70446
MA0055.11.40057
MA0056.10
MA0057.10.397382
MA0058.10.732537
MA0059.10.729981
MA0060.10.119532
MA0061.10.330174
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.11.95025
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.212523
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.730303
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.467716
MA0089.10
MA0090.10.792817
MA0091.10.351901
MA0092.10.852371
MA0093.10.61153
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.617985
MA0103.10.203171
MA0105.10.0403209
MA0106.10.482519
MA0107.10.475157
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.481808
MA0117.10.827487
MA0119.10.698186
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.13.18713
MA0136.11.14308
MA0139.10.307853
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.438224
MA0145.10.02761
MA0146.10.0935127
MA0147.10.488526
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.0944823
MA0138.21.323
MA0002.20.358551
MA0137.20.649788
MA0104.20.118985
MA0047.20.47109
MA0112.20.260758
MA0065.20.839576
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.11.41082
MA0155.10.74825
MA0156.10.654264
MA0157.10.576556
MA0158.10
MA0159.10.489747
MA0160.10.386031
MA0161.10
MA0162.10.0266618
MA0163.10.585549
MA0164.10.509774
MA0080.20.611699
MA0018.20.483823
MA0099.20.411824
MA0079.20.0235846
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

No analysis results for this cluster

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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