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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-3.12886773755974e

Latest revision as of 11:31, 17 September 2013


Full id: C805_granulocyte_acute_CD14_Eosinophils_Dendritic_Peripheral_Basophils



Phase1 CAGE Peaks

Hg19::chr11:67033909..67033950,+p1@ADRBK1
Hg19::chr11:67034140..67034180,+p2@ADRBK1
Hg19::chr17:73584515..73584582,+p1@MYO15B
Hg19::chr22:44577210..44577236,+p2@PARVG
Hg19::chr22:44577237..44577262,+p3@PARVG
Hg19::chr3:151962118..151962192,+p@chr3:151962118..151962192
+
Hg19::chr3:9851393..9851436,+p3@TTLL3
Hg19::chr6:167370049..167370094,-p2@RNASET2
Hg19::chrX:153191674..153191701,-p3@ARHGAP4
Hg19::chrX:153191709..153191767,-p2@ARHGAP4


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:0047696beta-adrenergic receptor kinase activity0.0211892456542427
GO:0022401adaptation of signaling pathway0.0211892456542427
GO:0002029desensitization of G-protein coupled receptor protein signaling pathway0.0211892456542427
GO:0045744negative regulation of G-protein coupled receptor protein signaling pathway0.0211892456542427
GO:0002026regulation of the force of heart contraction0.0296583952027233
GO:0004703G-protein coupled receptor kinase activity0.0458796346707017



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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell1.58e-76168
angioblastic mesenchymal cell1.58e-76168
hematopoietic cell6.17e-72177
hematopoietic oligopotent progenitor cell3.02e-71161
hematopoietic multipotent progenitor cell3.02e-71161
leukocyte3.96e-64136
hematopoietic lineage restricted progenitor cell4.01e-54120
nongranular leukocyte6.71e-54115
myeloid cell6.08e-46108
common myeloid progenitor6.08e-46108
myeloid leukocyte7.22e-3672
granulocyte monocyte progenitor cell1.92e-3267
myeloid lineage restricted progenitor cell3.37e-3166
macrophage dendritic cell progenitor1.44e-2961
monopoietic cell3.03e-2959
monocyte3.03e-2959
monoblast3.03e-2959
promonocyte3.03e-2959
defensive cell3.84e-2748
phagocyte3.84e-2748
classical monocyte3.36e-2542
CD14-positive, CD16-negative classical monocyte3.36e-2542
lymphocyte2.95e-2153
common lymphoid progenitor2.95e-2153
nucleate cell3.56e-2155
lymphoid lineage restricted progenitor cell6.13e-2152
T cell2.05e-1025
pro-T cell2.05e-1025
lymphocyte of B lineage2.06e-1024
pro-B cell2.06e-1024
mature alpha-beta T cell1.60e-0918
alpha-beta T cell1.60e-0918
immature T cell1.60e-0918
mature T cell1.60e-0918
immature alpha-beta T cell1.60e-0918
B cell1.42e-0814
stuff accumulating cell6.84e-0887
intermediate monocyte4.83e-079
CD14-positive, CD16-positive monocyte4.83e-079
mesenchymal cell6.08e-07354
CD8-positive, alpha-beta T cell8.50e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.02e-3898
blood island5.02e-3898
hemolymphoid system3.96e-33108
bone marrow1.12e-2876
immune system1.56e-2693
bone element6.20e-2582
skeletal element2.00e-1990
adult organism2.99e-19114
skeletal system2.17e-15100
lateral plate mesoderm1.14e-10203
blood1.77e-0715
haemolymphatic fluid1.77e-0715
organism substance1.77e-0715
Disease
Ontology termp-valuen
hematologic cancer1.22e-1251
immune system cancer1.22e-1251
leukemia3.46e-1239
myeloid leukemia1.59e-1031


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)
MA0003.15.81753
MA0004.10.380329
MA0006.11.23783
MA0007.10.952442
MA0009.10.828613
MA0014.10.954641
MA0017.10.744788
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
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.220931
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.867653
MA0056.10
MA0057.10.0580131
MA0058.10.293055
MA0059.10.291897
MA0060.10.430116
MA0061.10.377096
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.431725
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.79376
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.11.25978
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.10.189717
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.11.31824
MA0114.10.174997
MA0115.11.06753
MA0116.13.07162
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.11.21476
MA0139.10.716757
MA0140.10.437738
MA0141.10.789887
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.602634
MA0146.14.09727
MA0147.11.03863
MA0148.10.403564
MA0149.10.428597
MA0062.20.740103
MA0035.20.437071
MA0039.22.87101
MA0138.20.569505
MA0002.20.129981
MA0137.20.255808
MA0104.20.845907
MA0047.20.504873
MA0112.22.8109
MA0065.20.340764
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.0494985
MA0155.11.6917
MA0156.11.31919
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.14.5564
MA0163.14.49302
MA0164.10.544294
MA0080.21.24809
MA0018.20.517858
MA0099.21.12985
MA0079.22.02097
MA0102.21.36707
MA0258.10.919347
MA0259.10.560522
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
ELF1#199772.980668571165280.002378202870469130.0134738596934429
HMGN3#932454.08927386167530.004038023271587280.0193328647868939
PAX5#507953.334782765588910.009853624493675830.0370287380719276
POLR2A#5430102.147453176558070.0004793377491637920.00436380362490562
YY1#752873.43781952489770.0009684329216151120.00696283669974946
ZBTB7A#5134153.675954653937950.00645854601955880.0280502386050943



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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