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Coexpression cluster:C4250: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.0471418,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;3.13838,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;1.70328,MA0059.1;1.70014,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0185922,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.715722,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;1.84783,MA0093.1;1.55117,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;2.59836,MA0109.1;0,MA0111.1;0.767139,MA0113.1;2.29491,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.0526989,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.387745,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.00160703,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:55, 22 January 2013


Full id: C4250_Macrophage_CD14_lung_Monocytederived_Melanocyte_Dendritic_mature



Phase1 CAGE Peaks

Hg19::chr2:86110452..86110460,+p@chr2:86110452..86110460
+
Hg19::chr3:15382885..15382889,-p2@SH3BP5
Hg19::chr5:36680383..36680394,+p15@SLC1A3


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:0005313L-glutamate transmembrane transporter activity0.00900529667184184
GO:0001504neurotransmitter uptake0.00900529667184184
GO:0015172acidic amino acid transmembrane transporter activity0.00900529667184184
GO:0015813L-glutamate transport0.00900529667184184
GO:0015800acidic amino acid transport0.00900529667184184
GO:0017153sodium:dicarboxylate symporter activity0.00900529667184184
GO:0005310dicarboxylic acid transmembrane transporter activity0.00900529667184184
GO:0006835dicarboxylic acid transport0.00900529667184184
GO:0015179L-amino acid transmembrane transporter activity0.013686271723284
GO:0005343organic acid:sodium symporter activity0.013686271723284
GO:0015296anion:cation symporter activity0.013686271723284
GO:0004860protein kinase inhibitor activity0.013686271723284
GO:0019210kinase inhibitor activity0.013686271723284
GO:0005070SH3/SH2 adaptor activity0.0148252658539005
GO:0060090molecular adaptor activity0.0161167081592623
GO:0015171amino acid transmembrane transporter activity0.0161167081592623
GO:0006865amino acid transport0.0161167081592623
GO:0006836neurotransmitter transport0.0161167081592623
GO:0001505regulation of neurotransmitter levels0.0161167081592623
GO:0015837amine transport0.0161167081592623
GO:0015370solute:sodium symporter activity0.0161167081592623
GO:0030674protein binding, bridging0.0161167081592623
GO:0046943carboxylic acid transmembrane transporter activity0.0161167081592623
GO:0046942carboxylic acid transport0.0161167081592623
GO:0015849organic acid transport0.0161167081592623
GO:0005342organic acid transmembrane transporter activity0.0161167081592623
GO:0019887protein kinase regulator activity0.0164589308333072
GO:0015294solute:cation symporter activity0.0172292068078032
GO:0019207kinase regulator activity0.0178003717136349
GO:0008509anion transmembrane transporter activity0.0294397965576245
GO:0015293symporter activity0.0329724945737631
GO:0007268synaptic transmission0.0382505891715711
GO:0019226transmission of nerve impulse0.0421825913579477
GO:0015291secondary active transmembrane transporter activity0.0446441028060174
GO:0004857enzyme inhibitor activity0.0482784473309191



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
defensive cell3.66e-7848
phagocyte3.66e-7848
monopoietic cell8.29e-7659
monocyte8.29e-7659
monoblast8.29e-7659
promonocyte8.29e-7659
macrophage dendritic cell progenitor3.73e-7361
myeloid lineage restricted progenitor cell3.25e-6766
granulocyte monocyte progenitor cell3.93e-6667
classical monocyte4.39e-6542
CD14-positive, CD16-negative classical monocyte4.39e-6542
myeloid leukocyte3.69e-6172
stuff accumulating cell6.04e-4787
myeloid cell8.21e-39108
common myeloid progenitor8.21e-39108
nongranular leukocyte4.48e-36115
hematopoietic lineage restricted progenitor cell2.58e-34120
leukocyte1.53e-29136
hematopoietic oligopotent progenitor cell5.76e-24161
hematopoietic multipotent progenitor cell5.76e-24161
hematopoietic stem cell1.06e-22168
angioblastic mesenchymal cell1.06e-22168
hematopoietic cell3.22e-21177
macrophage2.79e-146
mesenchymal cell9.04e-10354
connective tissue cell1.91e-09361
motile cell2.68e-08386
immature conventional dendritic cell5.48e-085
common dendritic progenitor5.48e-085
multi fate stem cell6.75e-07427
Uber Anatomy
Ontology termp-valuen
bone marrow1.20e-5776
bone element5.20e-5382
immune system3.13e-4993
skeletal element8.85e-4890
hematopoietic system2.07e-4698
blood island2.07e-4698
skeletal system2.10e-42100
hemolymphoid system1.52e-41108
musculoskeletal system7.11e-23167
lateral plate mesoderm4.43e-19203
mesoderm6.33e-10315
mesoderm-derived structure6.33e-10315
presumptive mesoderm6.33e-10315
connective tissue7.87e-10371


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.13.13838
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.11.70328
MA0059.11.70014
MA0060.10.492218
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
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.11.84783
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.22.59836
MA0109.10
MA0111.10.767139
MA0113.12.29491
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
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
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
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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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