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Coexpression cluster:C1125: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 11:38, 17 September 2013


Full id: C1125_anaplastic_CD14_CD14CD16_acute_Macrophage_Dendritic_Monocytederived



Phase1 CAGE Peaks

Hg19::chr10:98416663..98416681,-p@chr10:98416663..98416681
-
Hg19::chr10:98416690..98416695,-p@chr10:98416690..98416695
-
Hg19::chr10:98416698..98416709,-p@chr10:98416698..98416709
-
Hg19::chr10:98416729..98416746,-p@chr10:98416729..98416746
-
Hg19::chr1:206945754..206945768,-p5@IL10
Hg19::chr7:112758720..112758727,+p@chr7:112758720..112758727
+
Hg19::chr9:92040335..92040353,-p@chr9:92040335..92040353
-


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
monopoietic cell8.89e-10559
monocyte8.89e-10559
monoblast8.89e-10559
promonocyte8.89e-10559
macrophage dendritic cell progenitor7.66e-10161
myeloid leukocyte2.76e-9672
defensive cell1.66e-9448
phagocyte1.66e-9448
myeloid lineage restricted progenitor cell4.94e-9266
granulocyte monocyte progenitor cell1.99e-9067
classical monocyte3.26e-8642
CD14-positive, CD16-negative classical monocyte3.26e-8642
myeloid cell5.81e-78108
common myeloid progenitor5.81e-78108
nongranular leukocyte5.15e-58115
leukocyte8.13e-54136
hematopoietic stem cell2.06e-53168
angioblastic mesenchymal cell2.06e-53168
hematopoietic oligopotent progenitor cell2.69e-51161
hematopoietic multipotent progenitor cell2.69e-51161
hematopoietic cell1.08e-49177
hematopoietic lineage restricted progenitor cell5.04e-49120
stuff accumulating cell1.92e-4587
intermediate monocyte4.40e-199
CD14-positive, CD16-positive monocyte4.40e-199
mesenchymal cell3.97e-15354
connective tissue cell1.80e-14361
motile cell3.60e-12386
macrophage1.48e-096
multi fate stem cell2.11e-09427
somatic stem cell5.02e-09433
stem cell1.53e-08441
non-classical monocyte2.76e-083
CD14-low, CD16-positive monocyte2.76e-083
basophil8.20e-073
Uber Anatomy
Ontology termp-valuen
bone marrow7.45e-7876
bone element5.43e-7182
hematopoietic system6.19e-7198
blood island6.19e-7198
immune system2.48e-7093
hemolymphoid system7.08e-65108
skeletal element2.96e-6390
skeletal system2.58e-55100
lateral plate mesoderm2.32e-27203
musculoskeletal system1.13e-26167
connective tissue3.04e-14371
mesoderm3.01e-12315
mesoderm-derived structure3.01e-12315
presumptive mesoderm3.01e-12315


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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.12.05477
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.11.46692
MA0052.12.07492
MA0055.10.0407081
MA0056.10
MA0057.10.744639
MA0058.11.04727
MA0059.11.04442
MA0060.10.638423
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.11.08222
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.9112
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.12.09327
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.708913
MA0145.10.0807715
MA0146.10.0610556
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.0170091
MA0138.20.704862
MA0002.21.79899
MA0137.21.70023
MA0104.20.223944
MA0047.20.636643
MA0112.20.556641
MA0065.21.48254
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.12.57306
MA0157.10.749547
MA0158.10
MA0159.10.770207
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.382702
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.23.51215
MA0079.20.000432051
MA0102.21.51913
MA0258.11.27333
MA0259.10.289405
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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