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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:40, 17 September 2013


Full id: C1238_CD34_CD14_Eosinophils_CD8_Natural_CD19_Peripheral



Phase1 CAGE Peaks

Hg19::chr19:1248314..1248335,+p9@MIDN
Hg19::chr1:2222149..2222184,-p@chr1:2222149..2222184
-
Hg19::chr1:2232428..2232442,-p@chr1:2232428..2232442
-
Hg19::chr1:2232455..2232495,-p@chr1:2232455..2232495
-
Hg19::chr1:2232583..2232594,-p@chr1:2232583..2232594
-
Hg19::chr3:114866901..114866924,+p@chr3:114866901..114866924
+
Hg19::chr8:41997529..41997538,+p@chr8:41997529..41997538
+


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
leukocyte8.12e-59136
hematopoietic stem cell1.07e-50168
angioblastic mesenchymal cell1.07e-50168
hematopoietic cell3.62e-47177
hematopoietic lineage restricted progenitor cell1.49e-46120
classical monocyte4.40e-4642
CD14-positive, CD16-negative classical monocyte4.40e-4642
myeloid leukocyte1.40e-4572
nongranular leukocyte1.98e-43115
hematopoietic oligopotent progenitor cell8.90e-43161
hematopoietic multipotent progenitor cell8.90e-43161
granulocyte monocyte progenitor cell1.91e-3967
defensive cell4.48e-3948
phagocyte4.48e-3948
myeloid lineage restricted progenitor cell4.89e-3866
myeloid cell3.33e-32108
common myeloid progenitor3.33e-32108
macrophage dendritic cell progenitor3.77e-3261
monopoietic cell1.73e-3159
monocyte1.73e-3159
monoblast1.73e-3159
promonocyte1.73e-3159
intermediate monocyte5.51e-199
CD14-positive, CD16-positive monocyte5.51e-199
stuff accumulating cell2.67e-1787
mesenchymal cell2.33e-14354
CD4-positive, alpha-beta T cell6.89e-146
connective tissue cell9.80e-14361
histamine secreting cell1.28e-115
biogenic amine secreting cell1.28e-115
granulocytopoietic cell1.28e-115
mast cell1.28e-115
mast cell progenitor1.28e-115
basophil mast progenitor cell1.28e-115
motile cell1.49e-11386
T cell1.77e-1025
pro-T cell1.77e-1025
lymphoid lineage restricted progenitor cell5.69e-1052
stem cell7.36e-10441
lymphocyte1.08e-0953
common lymphoid progenitor1.08e-0953
mature alpha-beta T cell3.05e-0918
alpha-beta T cell3.05e-0918
immature T cell3.05e-0918
mature T cell3.05e-0918
immature alpha-beta T cell3.05e-0918
nucleate cell3.60e-0955
multi fate stem cell6.30e-09427
somatic stem cell1.43e-08433
natural killer cell2.65e-083
pro-NK cell2.65e-083
single nucleate cell6.38e-083
mononuclear cell6.38e-083
basophil6.53e-083
naive T cell2.04e-073
plasmacytoid dendritic cell2.96e-073
granulocyte4.49e-078
non-classical monocyte9.30e-073
CD14-low, CD16-positive monocyte9.30e-073
Uber Anatomy
Ontology termp-valuen
bone marrow1.50e-3576
hematopoietic system1.47e-3398
blood island1.47e-3398
bone element4.12e-3282
immune system2.90e-3093
hemolymphoid system2.87e-29108
skeletal element3.04e-2890
skeletal system2.75e-24100
connective tissue6.91e-13371
musculoskeletal system2.90e-10167
lateral plate mesoderm5.89e-10203


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)
MA0003.10.546816
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.11.67472
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.940207
MA0029.10.886702
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
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.10.744639
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.11.71672
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.0282921
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.11.17914
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.332048
MA0105.12.29445
MA0106.10.648997
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.11.00897
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.11.38735
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.11.30855
MA0145.10.276317
MA0146.12.9475
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.22.39331
MA0035.20.564239
MA0039.20.243958
MA0138.20.704862
MA0002.21.15032
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.944394
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.910701
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.780982
MA0163.10.19677
MA0164.10.678332
MA0080.20.344472
MA0018.21.56673
MA0099.20.572
MA0079.20.07638
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
EBF1#187956.361762033263580.0003078439918611820.00316976423799566
ELF1#199753.041498542005380.009719562269370750.036568369316287
FOS#235367.712533121909491.19258382729196e-050.000301433355127166
FOSL1#8061211.34673706182090.01223664790675720.0443651763776231
PAX5#507954.763975379412740.001218821047007470.00820130476956465
RFX5#599346.884520472682910.001352207031528580.0089037986360137
SPI1#668844.688184862012990.005685680529144170.0256681416436106



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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