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Coexpression cluster:C1581: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:47, 17 September 2013


Full id: C1581_CD14_Basophils_Neutrophils_Eosinophils_Mast_Dendritic_Whole



Phase1 CAGE Peaks

Hg19::chr10:45914854..45914887,-p@chr10:45914854..45914887
-
Hg19::chr10:75571566..75571584,-p2@NDST2
Hg19::chr15:63414583..63414595,-p@chr15:63414583..63414595
-
Hg19::chr22:37309662..37309694,+p1@CSF2RB
Hg19::chr22:37319278..37319288,+p@chr22:37319278..37319288
+


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:0030526granulocyte macrophage colony-stimulating factor receptor complex0.00250787389551549
GO:0019978interleukin-3 binding0.00250787389551549
GO:0004912interleukin-3 receptor activity0.00250787389551549
GO:0004914interleukin-5 receptor activity0.00250787389551549
GO:0019980interleukin-5 binding0.00250787389551549
GO:0015016[heparan sulfate]-glucosamine N-sulfotransferase activity0.00278648553605186
GO:0015012heparan sulfate proteoglycan biosynthetic process0.00537354089379126
GO:0030201heparan sulfate proteoglycan metabolic process0.00626885419474033
GO:0030166proteoglycan biosynthetic process0.00928609767905773
GO:0006029proteoglycan metabolic process0.0110152288660697
GO:0007585respiratory gaseous exchange0.0110152288660697
GO:0004907interleukin receptor activity0.0118373341768045
GO:0019965interleukin binding0.0125316177331256
GO:0019221cytokine and chemokine mediated signaling pathway0.0125316177331256
GO:0044272sulfur compound biosynthetic process0.0125316177331256
GO:0008146sulfotransferase activity0.0135745195903601
GO:0016782transferase activity, transferring sulfur-containing groups0.0152307013251199
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0160069626551084
GO:0006790sulfur metabolic process0.0185765203393453
GO:0019838growth factor binding0.0185765203393453
GO:0019955cytokine binding0.0196768804642845
GO:0043235receptor complex0.0208660349762662
GO:0016051carbohydrate biosynthetic process0.0250289063122503



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
leukocyte4.12e-55136
myeloid leukocyte2.66e-5372
hematopoietic stem cell1.32e-49168
angioblastic mesenchymal cell1.32e-49168
hematopoietic cell1.95e-48177
granulocyte monocyte progenitor cell1.39e-4767
myeloid cell4.09e-47108
common myeloid progenitor4.09e-47108
hematopoietic oligopotent progenitor cell3.09e-46161
hematopoietic multipotent progenitor cell3.09e-46161
classical monocyte4.62e-4442
CD14-positive, CD16-negative classical monocyte4.62e-4442
myeloid lineage restricted progenitor cell1.93e-4266
macrophage dendritic cell progenitor3.93e-4161
defensive cell1.61e-4048
phagocyte1.61e-4048
hematopoietic lineage restricted progenitor cell4.56e-40120
monopoietic cell3.57e-3959
monocyte3.57e-3959
monoblast3.57e-3959
promonocyte3.57e-3959
nongranular leukocyte7.47e-37115
stuff accumulating cell1.62e-1787
mesenchymal cell2.43e-11354
dendritic cell4.46e-1110
connective tissue cell1.55e-10361
granulocyte4.24e-108
intermediate monocyte5.60e-109
CD14-positive, CD16-positive monocyte5.60e-109
conventional dendritic cell2.88e-098
blood cell2.95e-0811
motile cell8.02e-08386
multi fate stem cell1.53e-07427
stem cell1.81e-07441
somatic stem cell4.83e-07433
immature conventional dendritic cell7.43e-075
common dendritic progenitor7.43e-075
histamine secreting cell9.90e-075
biogenic amine secreting cell9.90e-075
granulocytopoietic cell9.90e-075
mast cell9.90e-075
mast cell progenitor9.90e-075
basophil mast progenitor cell9.90e-075
Uber Anatomy
Ontology termp-valuen
hemolymphoid system2.94e-47108
hematopoietic system1.09e-4598
blood island1.09e-4598
immune system9.17e-4293
bone marrow2.66e-3976
bone element8.11e-3582
skeletal element8.36e-3090
skeletal system1.01e-24100
lateral plate mesoderm2.89e-21203
musculoskeletal system4.34e-10167
connective tissue7.27e-10371
mesoderm1.30e-07315
mesoderm-derived structure1.30e-07315
presumptive mesoderm1.30e-07315


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)
MA0003.10.136928
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.11.66737
MA0058.10.523638
MA0059.11.29682
MA0060.10.321781
MA0061.13.05948
MA0063.10
MA0066.11.74614
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.111822
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.11.12656
MA0105.12.26263
MA0106.10.779931
MA0107.11.74965
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.12.64838
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.12.90482
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.22.8814
MA0138.20.837782
MA0002.20.30855
MA0137.21.20193
MA0104.20.858845
MA0047.20.767096
MA0112.21.35805
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.10.81299
MA0163.10.680296
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.26.20913
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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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