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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:17, 17 September 2013


Full id: C303_CD14_Basophils_Peripheral_Eosinophils_CD14CD16_Neutrophils_Whole



Phase1 CAGE Peaks

Hg19::chr10:135073029..135073042,+p@chr10:135073029..135073042
+
Hg19::chr11:64163297..64163310,-p1@ENST00000457725
Hg19::chr11:65220998..65221001,+p@chr11:65220998..65221001
+
Hg19::chr11:66888450..66888468,-p@chr11:66888450..66888468
-
Hg19::chr12:69747591..69747611,-p1@ENST00000548626
Hg19::chr13:99922932..99922946,-p@chr13:99922932..99922946
-
Hg19::chr13:99930136..99930140,+p1@AF339795
Hg19::chr13:99932682..99932704,+p@chr13:99932682..99932704
+
Hg19::chr13:99932706..99932716,+p@chr13:99932706..99932716
+
Hg19::chr13:99934075..99934096,-p@chr13:99934075..99934096
-
Hg19::chr14:75754624..75754635,+p@chr14:75754624..75754635
+
Hg19::chr17:7024749..7024764,-p@chr17:7024749..7024764
-
Hg19::chr17:7077590..7077615,-p@chr17:7077590..7077615
-
Hg19::chr17:7077620..7077625,-p@chr17:7077620..7077625
-
Hg19::chr17:72524949..72524975,+p@chr17:72524949..72524975
+
Hg19::chr17:72774120..72774160,-p@chr17:72774120..72774160
-
Hg19::chr17:72776484..72776500,+p@chr17:72776484..72776500
+
Hg19::chr17:72776516..72776526,+p@chr17:72776516..72776526
+
Hg19::chr17:81060279..81060283,-p@chr17:81060279..81060283
-
Hg19::chr17:81101323..81101338,+p@chr17:81101323..81101338
+
Hg19::chr17:81103271..81103285,-p@chr17:81103271..81103285
-
Hg19::chr17:81103526..81103542,+p@chr17:81103526..81103542
+
Hg19::chr17:81147900..81147911,+p@chr17:81147900..81147911
+
Hg19::chr1:10057123..10057149,+p3@RBP7
Hg19::chr22:37976067..37976079,-p3@LGALS2
Hg19::chr2:230162106..230162117,-p@chr2:230162106..230162117
-
Hg19::chr2:230162122..230162143,-p@chr2:230162122..230162143
-
Hg19::chr5:139631154..139631161,-p@chr5:139631154..139631161
-
Hg19::chr5:139725653..139725678,-p@chr5:139725653..139725678
-
Hg19::chr6:11537600..11537651,-p@chr6:11537600..11537651
-
Hg19::chr6:163826254..163826261,+p@chr6:163826254..163826261
+
Hg19::chr6:163827012..163827025,-p@chr6:163827012..163827025
-
Hg19::chr7:2774708..2774727,-p@chr7:2774708..2774727
-
Hg19::chr7:2797828..2797848,-p@chr7:2797828..2797848
-
Hg19::chr8:48273366..48273391,+p3@KIAA0146
Hg19::chr8:48273416..48273419,+p15@KIAA0146
Hg19::chr8:48282088..48282092,-p@chr8:48282088..48282092
-
Hg19::chr8:48513543..48513562,+p@chr8:48513543..48513562
+
Hg19::chr8:48540690..48540694,+p@chr8:48540690..48540694
+
Hg19::chr9:27701766..27701787,-p@chr9:27701766..27701787
-


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:0019841retinol binding0.00425250120614753
GO:0016918retinal binding0.00425250120614753
GO:0005501retinoid binding0.00425250120614753
GO:0019840isoprenoid binding0.00425250120614753
GO:0005625soluble fraction0.0407202229474492
GO:0019842vitamin binding0.0407202229474492
GO:0005529sugar binding0.0493596312651508



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
classical monocyte3.31e-14142
CD14-positive, CD16-negative classical monocyte3.31e-14142
defensive cell1.50e-12248
phagocyte1.50e-12248
monopoietic cell2.00e-9659
monocyte2.00e-9659
monoblast2.00e-9659
promonocyte2.00e-9659
macrophage dendritic cell progenitor4.71e-9361
myeloid leukocyte5.84e-9272
myeloid lineage restricted progenitor cell1.67e-8566
granulocyte monocyte progenitor cell3.97e-8467
stuff accumulating cell5.64e-6487
nongranular leukocyte1.27e-60115
myeloid cell8.24e-59108
common myeloid progenitor8.24e-59108
leukocyte1.43e-58136
hematopoietic lineage restricted progenitor cell7.45e-49120
hematopoietic stem cell7.82e-46168
angioblastic mesenchymal cell7.82e-46168
hematopoietic cell4.49e-43177
hematopoietic oligopotent progenitor cell5.64e-41161
hematopoietic multipotent progenitor cell5.64e-41161
intermediate monocyte1.14e-399
CD14-positive, CD16-positive monocyte1.14e-399
mesenchymal cell3.70e-17354
connective tissue cell1.19e-16361
motile cell7.27e-15386
basophil3.45e-143
single nucleate cell3.77e-143
mononuclear cell3.77e-143
non-classical monocyte9.89e-143
CD14-low, CD16-positive monocyte9.89e-143
multi fate stem cell1.12e-12427
somatic stem cell2.24e-12433
stem cell5.52e-12441
circulating cell2.77e-076
Uber Anatomy
Ontology termp-valuen
bone marrow2.42e-7376
bone element1.88e-6782
hematopoietic system1.38e-6598
blood island1.38e-6598
skeletal element8.37e-6190
hemolymphoid system8.52e-59108
immune system1.33e-5893
skeletal system5.67e-54100
musculoskeletal system3.68e-29167
lateral plate mesoderm1.93e-27203
connective tissue5.84e-16371
mesoderm1.16e-15315
mesoderm-derived structure1.16e-15315
presumptive mesoderm1.16e-15315


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)
MA0003.15.95384e-05
MA0004.10.197652
MA0006.10.339054
MA0007.10.401399
MA0009.11.56036
MA0014.10.0431521
MA0017.10.0906026
MA0019.10.375827
MA0024.10.247435
MA0025.11.10005
MA0027.11.83568
MA0028.10.0162592
MA0029.10.261061
MA0030.10.252948
MA0031.10.208976
MA0038.10.652865
MA0040.10.265236
MA0041.10.060153
MA0042.10.183871
MA0043.10.866754
MA0046.10.315924
MA0048.10.5274
MA0050.11.11833
MA0051.11.07288
MA0052.10.738956
MA0055.10.508167
MA0056.10
MA0057.10.0375806
MA0058.10.0259464
MA0059.10.108631
MA0060.10.050737
MA0061.10.0338355
MA0063.10
MA0066.10.0957332
MA0067.11.437
MA0068.10.046417
MA0069.10.313005
MA0070.10.30458
MA0071.10.96175
MA0072.10.814517
MA0073.12.13299e-05
MA0074.10.0932113
MA0076.10.0297509
MA0077.10.295472
MA0078.10.445005
MA0081.10.493777
MA0083.10.329963
MA0084.10.758508
MA0087.10.299389
MA0088.10.202426
MA0089.10
MA0090.10.135009
MA0091.10.772511
MA0092.10.042021
MA0093.10.345973
MA0095.10
MA0098.10
MA0100.10.683998
MA0101.10.0685984
MA0103.10.0593229
MA0105.10.00316096
MA0106.10.115825
MA0107.10.0313847
MA0108.20.596523
MA0109.10
MA0111.10.340952
MA0113.10.392846
MA0114.10.345217
MA0115.10.52159
MA0116.10.0327648
MA0117.11.66299
MA0119.10.022147
MA0122.10.373764
MA0124.10.485991
MA0125.10.415795
MA0130.10
MA0131.10.155349
MA0132.10
MA0133.10
MA0135.10.347651
MA0136.10.668644
MA0139.10.254598
MA0140.10.265991
MA0141.10.107262
MA0142.10.188476
MA0143.10.393088
MA0144.10.306198
MA0145.10.101436
MA0146.10.000283793
MA0147.10.213741
MA0148.10.224417
MA0149.10.0730455
MA0062.20.0310062
MA0035.20.0767782
MA0039.20.00285736
MA0138.20.145586
MA0002.21.00841
MA0137.20.0173938
MA0104.20.226941
MA0047.20.354428
MA0112.20.0475457
MA0065.20.0605035
MA0150.10.561922
MA0151.10
MA0152.10.27382
MA0153.10.402047
MA0154.10.547086
MA0155.10.126474
MA0156.10.397124
MA0157.10.510953
MA0158.10
MA0159.11.9358
MA0160.10.0684362
MA0161.10
MA0162.10.00127136
MA0163.10.00200041
MA0164.10.40999
MA0080.21.21571
MA0018.20.372456
MA0099.20.274248
MA0079.21.56144e-09
MA0102.20.793085
MA0258.10.151519
MA0259.10.22971
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
BATF#1053863.653670268845550.00552249746409360.0250027792895991
IRF4#366273.835039720180220.002030474904189920.0117949145402242



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

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