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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.0444409901401481,

Latest revision as of 12:33, 17 September 2013


Full id: C3790_Neutrophils_Eosinophils_Mesenchymal_Whole_Alveolar_blood_CD14



Phase1 CAGE Peaks

Hg19::chr19:41082755..41082801,+p1@SHKBP1
Hg19::chr7:100450328..100450398,+p1@SLC12A9
Hg19::chr7:128050027..128050053,-p2@IMPDH1


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:0003938IMP dehydrogenase activity0.0128031549908582
GO:0046037GMP metabolic process0.0128031549908582
GO:0006177GMP biosynthetic process0.0128031549908582
GO:0009168purine ribonucleoside monophosphate biosynthetic process0.0224329571967736
GO:0009167purine ribonucleoside monophosphate metabolic process0.0224329571967736
GO:0009127purine nucleoside monophosphate biosynthetic process0.0224329571967736
GO:0009126purine nucleoside monophosphate metabolic process0.0224329571967736
GO:0009161ribonucleoside monophosphate metabolic process0.0224329571967736
GO:0009156ribonucleoside monophosphate biosynthetic process0.0224329571967736
GO:0006183GTP biosynthetic process0.0224329571967736
GO:0046039GTP metabolic process0.0224329571967736
GO:0009124nucleoside monophosphate biosynthetic process0.0224329571967736
GO:0009123nucleoside monophosphate metabolic process0.0224329571967736
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.0403744453611115
GO:0009145purine nucleoside triphosphate biosynthetic process0.0403744453611115
GO:0009201ribonucleoside triphosphate biosynthetic process0.0403744453611115
GO:0008076voltage-gated potassium channel complex0.0403744453611115
GO:0009142nucleoside triphosphate biosynthetic process0.0403744453611115
GO:0009205purine ribonucleoside triphosphate metabolic process0.0403744453611115
GO:0009144purine nucleoside triphosphate metabolic process0.0403744453611115
GO:0009199ribonucleoside triphosphate metabolic process0.0403744453611115
GO:0030955potassium ion binding0.0403744453611115
GO:0009152purine ribonucleotide biosynthetic process0.0403744453611115
GO:0009141nucleoside triphosphate metabolic process0.0403744453611115
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0403744453611115
GO:0009150purine ribonucleotide metabolic process0.0403744453611115
GO:0009260ribonucleotide biosynthetic process0.0403744453611115
GO:0006164purine nucleotide biosynthetic process0.0403744453611115
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0403744453611115
GO:0005249voltage-gated potassium channel activity0.0403744453611115
GO:0006163purine nucleotide metabolic process0.0403744453611115
GO:0009259ribonucleotide metabolic process0.0403744453611115
GO:0005267potassium channel activity0.0472803330340079
GO:0031420alkali metal ion binding0.0472803330340079
GO:0007601visual perception0.0472803330340079
GO:0050953sensory perception of light stimulus0.0472803330340079



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
leukocyte1.87e-31136
myeloid leukocyte3.26e-3172
nongranular leukocyte2.53e-30115
monopoietic cell5.47e-3059
monocyte5.47e-3059
monoblast5.47e-3059
promonocyte5.47e-3059
macrophage dendritic cell progenitor1.35e-2961
defensive cell3.14e-2848
phagocyte3.14e-2848
granulocyte monocyte progenitor cell1.85e-2667
somatic cell1.09e-25588
classical monocyte2.59e-2542
CD14-positive, CD16-negative classical monocyte2.59e-2542
hematopoietic lineage restricted progenitor cell1.12e-24120
myeloid lineage restricted progenitor cell8.81e-2466
hematopoietic stem cell1.78e-23168
angioblastic mesenchymal cell1.78e-23168
hematopoietic oligopotent progenitor cell3.39e-23161
hematopoietic multipotent progenitor cell3.39e-23161
hematopoietic cell5.23e-23177
myeloid cell1.13e-19108
common myeloid progenitor1.13e-19108
multi fate stem cell3.27e-17427
somatic stem cell4.73e-17433
native cell6.99e-17722
connective tissue cell1.25e-16361
stem cell3.47e-16441
stuff accumulating cell4.90e-1687
mesenchymal cell2.11e-15354
motile cell1.45e-13386
animal cell3.12e-10679
eukaryotic cell3.12e-10679
intermediate monocyte6.93e-079
CD14-positive, CD16-positive monocyte6.93e-079
Uber Anatomy
Ontology termp-valuen
hemolymphoid system7.11e-32108
hematopoietic system1.82e-3198
blood island1.82e-3198
lateral plate mesoderm1.56e-29203
immune system2.55e-2793
bone marrow2.37e-2676
bone element5.68e-2482
skeletal element1.56e-2290
skeletal system6.89e-20100
mesoderm1.41e-17315
mesoderm-derived structure1.41e-17315
presumptive mesoderm1.41e-17315
musculoskeletal system3.08e-17167
connective tissue7.72e-16371


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)
MA0003.12.05336
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.13.21605
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.11.16674
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.90288
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
IRF1#365937.63716375356390.002244692747297240.0128035754142532
NFYA#4800212.28372046655370.008516011403724430.0324753976336793
NFYB#4801211.17319550235760.01025467135054530.0381310791889343
SIN3A#2594235.408884726815140.006318961977991520.0276672146069449



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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