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Coexpression cluster:C438: Difference between revisions

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{{Coexpression_clusters
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|full_id=C438_skeletal_salivary_tridermal_mixed_seminal_Neutrophils_Melanocyte
|id=C438
}}

Latest revision as of 11:23, 17 September 2013


Full id: C438_skeletal_salivary_tridermal_mixed_seminal_Neutrophils_Melanocyte



Phase1 CAGE Peaks

Hg19::chr10:101198808..101198830,+p@chr10:101198808..101198830
+
Hg19::chr11:77597592..77597628,+p@chr11:77597592..77597628
+
Hg19::chr11:85195054..85195110,+p1@ENST00000463796
Hg19::chr12:104319932..104319960,-p@chr12:104319932..104319960
-
Hg19::chr14:23987059..23987091,-p1@ENST00000485514
Hg19::chr16:33963160..33963183,+p@chr16:33963160..33963183
+
Hg19::chr17:33478201..33478210,-p@chr17:33478201..33478210
-
Hg19::chr19:10778444..10778456,+p1@ENST00000516198
Hg19::chr19:55390072..55390098,-p@chr19:55390072..55390098
-
Hg19::chr2:133013092..133013149,-p@chr2:133013092..133013149
-
Hg19::chr2:133036750..133036762,-p@chr2:133036750..133036762
-
Hg19::chr2:133038991..133039032,-p@chr2:133038991..133039032
-
Hg19::chr2:133039111..133039124,-p@chr2:133039111..133039124
-
Hg19::chr2:159440717..159440733,-p@chr2:159440717..159440733
-
Hg19::chr2:159440775..159440800,-p@chr2:159440775..159440800
-
Hg19::chr3:117985764..117985778,+p@chr3:117985764..117985778
+
Hg19::chr4:70296681..70296712,-p1@ENST00000474870
Hg19::chr4:70296745..70296765,-p2@ENST00000474870
Hg19::chr7:68527367..68527388,+p1@ENST00000516439
Hg19::chr7:80963018..80963051,+p@chr7:80963018..80963051
+
Hg19::chr8:109304651..109304677,-p1@ENST00000476900
Hg19::chr8:69218504..69218531,-p@chr8:69218504..69218531
-


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
macrophage dendritic cell progenitor4.41e-0961
granulocyte monocyte progenitor cell1.06e-0867
monopoietic cell2.20e-0859
monocyte2.20e-0859
monoblast2.20e-0859
promonocyte2.20e-0859
myeloid leukocyte3.61e-0872
myeloid lineage restricted progenitor cell3.75e-0866
defensive cell9.19e-0848
phagocyte9.19e-0848
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm1.64e-11203
mesoderm3.29e-09315
mesoderm-derived structure3.29e-09315
presumptive mesoderm3.29e-09315
bone element9.70e-0882
bone marrow1.53e-0776
musculoskeletal system1.82e-07167
hematopoietic system9.50e-0798
blood island9.50e-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)
MA0003.12.30618e-05
MA0004.10.478761
MA0006.10.0694838
MA0007.10.449227
MA0009.10.526253
MA0014.10.0223655
MA0017.10.0884918
MA0019.10.262545
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.10.0770177
MA0029.10.450974
MA0030.10.441064
MA0031.10.386141
MA0038.10.22896
MA0040.10.456051
MA0041.10.98026
MA0042.10.457543
MA0043.10.526535
MA0046.10.516541
MA0048.10.0852241
MA0050.10.150446
MA0051.10.22589
MA0052.10.459414
MA0055.10.0249719
MA0056.10
MA0057.10.00450362
MA0058.10.101748
MA0059.10.331581
MA0060.10.109486
MA0061.10.0847828
MA0063.10
MA0066.10.22927
MA0067.10.820123
MA0068.10.0112936
MA0069.10.51311
MA0070.10.503171
MA0071.10.201311
MA0072.10.499187
MA0073.11.00961e-08
MA0074.10.225345
MA0076.10.110503
MA0077.10.49237
MA0078.10.814281
MA0081.10.679272
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.10.154793
MA0089.10
MA0090.11.24237
MA0091.10.160096
MA0092.10.136418
MA0093.10.530993
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.538883
MA0103.10.501795
MA0105.10.020431
MA0106.10.259598
MA0107.10.369945
MA0108.20.383574
MA0109.10
MA0111.10.398557
MA0113.10.272101
MA0114.10.0401034
MA0115.10.747865
MA0116.10.0431675
MA0117.10.560027
MA0119.10.308642
MA0122.10.583485
MA0124.11.6886
MA0125.11.52629
MA0130.10
MA0131.10.315517
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.10.234116
MA0139.10.0745458
MA0140.10.199454
MA0141.10.100114
MA0142.10.945139
MA0143.10.272236
MA0144.10.140794
MA0145.10.0933513
MA0146.10.000466837
MA0147.10.170045
MA0148.11.58312
MA0149.10.192747
MA0062.20.0177333
MA0035.20.198962
MA0039.24.36627e-05
MA0138.20.302079
MA0002.21.0893
MA0137.20.0801516
MA0104.20.108753
MA0047.21.29176
MA0112.20.00138028
MA0065.20.00177701
MA0150.10.369323
MA0151.10
MA0152.10.20405
MA0153.10.615584
MA0154.10.00323928
MA0155.10.00810476
MA0156.10.0812668
MA0157.10.337287
MA0158.10
MA0159.10.386598
MA0160.10.18494
MA0161.10
MA0162.10.000506716
MA0163.10.0253576
MA0164.10.28168
MA0080.20.0709213
MA0018.20.260646
MA0099.20.204301
MA0079.26.95859e-13
MA0102.21.03595
MA0258.10.032189
MA0259.10.713194
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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