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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:32, 17 September 2013


Full id: C847_Monocytederived_CD14_Macrophage_Dendritic_immature_adipose_lung



Phase1 CAGE Peaks

Hg19::chr19:11689703..11689718,-p4@ACP5
Hg19::chr19:11689732..11689743,-p7@ACP5
Hg19::chr19:51628330..51628379,+p1@SIGLEC9
Hg19::chr19:51628390..51628400,+p4@SIGLEC9
Hg19::chr19:52298383..52298398,+p2@FPR3
Hg19::chr19:52298399..52298445,+p1@FPR3
Hg19::chr19:52298453..52298460,+p3@FPR3
Hg19::chr19:52299474..52299504,-p@chr19:52299474..52299504
-
Hg19::chr22:39926179..39926203,-p@chr22:39926179..39926203
-
Hg19::chr3:152880098..152880109,+p2@RAP2B


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
granulocyte monocyte progenitor cell6.64e-7767
macrophage dendritic cell progenitor7.30e-7561
myeloid lineage restricted progenitor cell2.36e-7266
monopoietic cell1.05e-7159
monocyte1.05e-7159
monoblast1.05e-7159
promonocyte1.05e-7159
myeloid leukocyte6.03e-7072
defensive cell6.99e-6848
phagocyte6.99e-6848
classical monocyte4.09e-5742
CD14-positive, CD16-negative classical monocyte4.09e-5742
myeloid cell7.03e-51108
common myeloid progenitor7.03e-51108
leukocyte3.97e-45136
hematopoietic lineage restricted progenitor cell6.01e-39120
nongranular leukocyte7.35e-37115
hematopoietic stem cell1.48e-33168
angioblastic mesenchymal cell1.48e-33168
hematopoietic oligopotent progenitor cell6.35e-31161
hematopoietic multipotent progenitor cell6.35e-31161
hematopoietic cell9.12e-31177
stuff accumulating cell1.94e-3087
conventional dendritic cell2.21e-148
dendritic cell5.66e-1410
macrophage5.78e-126
immature conventional dendritic cell1.07e-105
common dendritic progenitor1.07e-105
Langerhans cell2.77e-085
intermediate monocyte5.07e-089
CD14-positive, CD16-positive monocyte5.07e-089
mesenchymal cell3.39e-07354
adult endothelial progenitor cell9.52e-073
connective tissue cell9.89e-07361
Uber Anatomy
Ontology termp-valuen
bone marrow1.38e-6576
immune system8.98e-6393
hematopoietic system1.47e-6298
blood island1.47e-6298
bone element2.05e-5982
hemolymphoid system6.19e-59108
skeletal element1.82e-5290
skeletal system2.38e-45100
lateral plate mesoderm3.55e-26203
musculoskeletal system1.28e-23167
mesoderm8.76e-15315
mesoderm-derived structure8.76e-15315
presumptive mesoderm8.76e-15315
adult organism7.04e-12114
organ8.22e-10503
germ layer4.26e-07560
germ layer / neural crest4.26e-07560
embryonic tissue4.26e-07560
presumptive structure4.26e-07560
germ layer / neural crest derived structure4.26e-07560
epiblast (generic)4.26e-07560
embryonic structure7.11e-07564


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)
MA0003.10.1987
MA0004.10.380329
MA0006.10.236135
MA0007.11.69684
MA0009.10.828613
MA0014.11.2642
MA0017.12.10084
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.963243
MA0043.10.828925
MA0046.10.817858
MA0048.10.830349
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.13.59645
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.848451
MA0061.10.377096
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.13.13273
MA0071.10.440254
MA0072.10.798564
MA0073.10.00880943
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.300184
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.646502
MA0105.10.189717
MA0106.10.516528
MA0107.10.529721
MA0108.20.666881
MA0109.10
MA0111.10.885497
MA0113.10.532314
MA0114.10.51954
MA0115.11.06753
MA0116.11.62509
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.12.16975
MA0130.10
MA0131.11.43152
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.11.21476
MA0139.10.353333
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.491079
MA0145.10.602634
MA0146.10.128432
MA0147.10.543675
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.936681
MA0138.21.39695
MA0002.20.129981
MA0137.20.710884
MA0104.20.138396
MA0047.20.504873
MA0112.20.133417
MA0065.20.340764
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.185581
MA0155.10.866026
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.544949
MA0160.10.417847
MA0161.10
MA0162.10.229496
MA0163.10.0728181
MA0164.10.544294
MA0080.20.671553
MA0018.20.517858
MA0099.20.444294
MA0079.20.227142
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
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
GATA3#262538.17095490716180.004888573999674950.0228765023726163
MAFF#23764211.2630712979890.01290318508912210.0464080083863497



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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