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Coexpression cluster:C236: Difference between revisions

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{{Coexpression_clusters
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60848,MA0019.1;1.19317,MA0024.1;0.150131,MA0025.1;0.823085,MA0027.1;1.6684,MA0028.1;0.144668,MA0029.1;0.161009,MA0030.1;1.46475,MA0031.1;0.766324,MA0038.1;0.161161,MA0040.1;2.17832,MA0041.1;0.0950971,MA0042.1;0.193092,MA0043.1;0.213202,MA0046.1;0.594332,MA0048.1;0.122591,MA0050.1;0.194227,MA0051.1;0.157417,MA0052.1;0.498991,MA0055.1;0.0147252,MA0056.1;0,MA0057.1;0.00274634,MA0058.1;0.00656227,MA0059.1;0.00645491,MA0060.1;0.000208656,MA0061.1;0.0136793,MA0063.1;0,MA0066.1;0.161542,MA0067.1;0.4486,MA0068.1;0.284316,MA0069.1;0.588518,MA0070.1;0.571737,MA0071.1;0.30415,MA0072.1;0.193792,MA0073.1;56.7161,MA0074.1;0.156755,MA0076.1;0.117728,MA0077.1;0.189042,MA0078.1;0.927119,MA0081.1;0.0348384,MA0083.1;0.217849,MA0084.1;0.6087,MA0087.1;0.561402,MA0088.1;0.000692932,MA0089.1;0,MA0090.1;0.272498,MA0091.1;0.674691,MA0092.1;0.166183,MA0093.1;0.0027172,MA0095.1;0,MA0098.1;0,MA0100.1;0.0456513,MA0101.1;0.131708,MA0103.1;0.112297,MA0105.1;0.000457953,MA0106.1;0.0542605,MA0107.1;0.0550249,MA0108.2;2.44919,MA0109.1;0,MA0111.1;0.147308,MA0113.1;0.2165,MA0114.1;0.323021,MA0115.1;1.00523,MA0116.1;0.00574254,MA0117.1;0.668877,MA0119.1;0.087219,MA0122.1;0.255297,MA0124.1;0.934011,MA0125.1;0.291999,MA0130.1;0,MA0131.1;0.0808893,MA0132.1;0,MA0133.1;0,MA0135.1;1.22541,MA0136.1;0.38035,MA0139.1;0.00301568,MA0140.1;0.0308744,MA0141.1;0.0997393,MA0142.1;0.696374,MA0143.1;0.216681,MA0144.1;0.0147327,MA0145.1;9.56752e-05,MA0146.1;1.05037e-05,MA0147.1;0.00612796,MA0148.1;0.462701,MA0149.1;0.0286403,MA0062.2;0.0309256,MA0035.2;0.549044,MA0039.2;7.83154e-12,MA0138.2;0.257603,MA0002.2;0.0932517,MA0137.2;0.0216886,MA0104.2;0.000204242,MA0047.2;0.41952,MA0112.2;6.47023e-05,MA0065.2;0.0188846,MA0150.1;0.0452139,MA0151.1;0,MA0152.1;0.896147,MA0153.1;1.40073,MA0154.1;0.000406519,MA0155.1;0.00064931,MA0156.1;0.470033,MA0157.1;0.637835,MA0158.1;0,MA0159.1;0.0233099,MA0160.1;0.267542,MA0161.1;0,MA0162.1;2.08474e-07,MA0163.1;1.42172e-06,MA0164.1;0.0642528,MA0080.2;0.242062,MA0018.2;0.0547185,MA0099.2;0.310947,MA0079.2;0,MA0102.2;0.641748,MA0258.1;0.0123158,MA0259.1;0.00100083,MA0442.1;0}}
|full_id=C236_CD14_Neutrophils_Monocytederived_renal_Eosinophils_testis_mesothelioma
|id=C236
|ontology_enrichment_celltype=CL:0000860!3.00e-24!45;CL:0002057!4.12e-24!42;CL:0000766!8.95e-24!76;CL:0002009!4.86e-23!65;CL:0002194!3.53e-22!63;CL:0000576!3.53e-22!63;CL:0000040!3.53e-22!63;CL:0000559!3.53e-22!63;CL:0000557!1.52e-20!71;CL:0000763!3.30e-20!112;CL:0000049!3.30e-20!112;CL:0000839!8.12e-20!70;CL:0000738!1.29e-17!140;CL:0000037!2.41e-15!172;CL:0000566!2.41e-15!172;CL:0002032!2.43e-15!165;CL:0000837!2.43e-15!165;CL:0002087!5.23e-15!119;CL:0002031!2.98e-13!124;CL:0000988!3.07e-13!182
|ontology_enrichment_disease=DOID:162!7.38e-08!235;DOID:14566!1.25e-07!239
|ontology_enrichment_uberon=UBERON:0002390!7.02e-17!102;UBERON:0003061!7.02e-17!102;UBERON:0002371!1.21e-15!80;UBERON:0002193!1.39e-14!112;UBERON:0001474!4.26e-14!86;UBERON:0004765!7.69e-11!101;UBERON:0001434!7.69e-11!101;UBERON:0002405!7.86e-09!115
}}

Latest revision as of 11:02, 17 September 2013


Full id: C236_CD14_Neutrophils_Monocytederived_renal_Eosinophils_testis_mesothelioma



Phase1 CAGE Peaks

Hg19::chr10:121154492..121154507,-p@chr10:121154492..121154507
-
Hg19::chr11:35228220..35228226,+p@chr11:35228220..35228226
+
Hg19::chr11:60183051..60183054,+p7@MS4A14
Hg19::chr11:9207433..9207444,-p@chr11:9207433..9207444
-
Hg19::chr11:9207504..9207519,-p@chr11:9207504..9207519
-
Hg19::chr11:9207544..9207563,-p@chr11:9207544..9207563
-
Hg19::chr11:9224733..9224747,-p@chr11:9224733..9224747
-
Hg19::chr12:90028637..90028650,-p@chr12:90028637..90028650
-
Hg19::chr14:35270349..35270367,-p@chr14:35270349..35270367
-
Hg19::chr14:35270378..35270401,-p@chr14:35270378..35270401
-
Hg19::chr15:39673743..39673750,-p@chr15:39673743..39673750
-
Hg19::chr15:45753568..45753592,+p@chr15:45753568..45753592
+
Hg19::chr15:45753821..45753832,+p@chr15:45753821..45753832
+
Hg19::chr15:45754126..45754155,+p@chr15:45754126..45754155
+
Hg19::chr15:45755889..45755934,+p@chr15:45755889..45755934
+
Hg19::chr16:55851797..55851809,-p@chr16:55851797..55851809
-
Hg19::chr17:49098687..49098705,-p@chr17:49098687..49098705
-
Hg19::chr17:72607351..72607373,-p@chr17:72607351..72607373
-
Hg19::chr17:76537739..76537756,-p@chr17:76537739..76537756
-
Hg19::chr18:61656025..61656039,+p@chr18:61656025..61656039
+
Hg19::chr18:61656066..61656085,+p@chr18:61656066..61656085
+
Hg19::chr19:52302728..52302742,-p@chr19:52302728..52302742
-
Hg19::chr19:54778385..54778415,-p@chr19:54778385..54778415
-
Hg19::chr19:55401699..55401714,+p@chr19:55401699..55401714
+
Hg19::chr1:157094541..157094547,-p@chr1:157094541..157094547
-
Hg19::chr1:160673803..160673806,-p@chr1:160673803..160673806
-
Hg19::chr20:30680206..30680216,+p@chr20:30680206..30680216
+
Hg19::chr21:37741568..37741572,+p2@MORC3
Hg19::chr21:45578064..45578104,-p@chr21:45578064..45578104
-
Hg19::chr2:143689349..143689367,+p@chr2:143689349..143689367
+
Hg19::chr2:143690337..143690349,+p@chr2:143690337..143690349
+
Hg19::chr2:143691180..143691192,+p@chr2:143691180..143691192
+
Hg19::chr2:143691203..143691217,+p@chr2:143691203..143691217
+
Hg19::chr2:143693415..143693427,+p@chr2:143693415..143693427
+
Hg19::chr2:143693429..143693450,+p@chr2:143693429..143693450
+
Hg19::chr2:143719228..143719232,+p@chr2:143719228..143719232
+
Hg19::chr3:10266052..10266067,+p@chr3:10266052..10266067
+
Hg19::chr3:10266146..10266158,+p@chr3:10266146..10266158
+
Hg19::chr3:10266234..10266276,+p@chr3:10266234..10266276
+
Hg19::chr3:10266288..10266301,+p@chr3:10266288..10266301
+
Hg19::chr3:170079070..170079087,+p@chr3:170079070..170079087
+
Hg19::chr3:170108089..170108122,+p@chr3:170108089..170108122
+
Hg19::chr3:170108158..170108171,+p@chr3:170108158..170108171
+
Hg19::chr3:33868462..33868472,+p@chr3:33868462..33868472
+
Hg19::chr3:39188734..39188759,+p@chr3:39188734..39188759
+
Hg19::chr3:72147410..72147424,-p@chr3:72147410..72147424
-
Hg19::chr3:72428522..72428552,-p2@RYBP
Hg19::chr4:122600725..122600738,-p@chr4:122600725..122600738
-
Hg19::chr4:122600766..122600777,-p@chr4:122600766..122600777
-
Hg19::chr4:139135048..139135078,-p@chr4:139135048..139135078
-
Hg19::chr4:139135635..139135651,-p@chr4:139135635..139135651
-
Hg19::chr4:139140415..139140423,-p@chr4:139140415..139140423
-
Hg19::chr4:169307206..169307214,-p@chr4:169307206..169307214
-
Hg19::chr5:150472940..150472943,+p@chr5:150472940..150472943
+
Hg19::chr6:116736718..116736735,+p@chr6:116736718..116736735
+
Hg19::chr6:2895616..2895628,-p@chr6:2895616..2895628
-
Hg19::chr7:154997905..154997916,-p@chr7:154997905..154997916
-
Hg19::chr8:134926792..134926802,-p@chr8:134926792..134926802
-
Hg19::chr8:79754868..79754882,+p@chr8:79754868..79754882
+


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
classical monocyte2.89e-13642
CD14-positive, CD16-negative classical monocyte2.89e-13642
defensive cell1.75e-11848
phagocyte1.75e-11848
monopoietic cell1.40e-9359
monocyte1.40e-9359
monoblast1.40e-9359
promonocyte1.40e-9359
macrophage dendritic cell progenitor2.30e-9061
myeloid lineage restricted progenitor cell3.62e-8366
granulocyte monocyte progenitor cell7.43e-8267
myeloid leukocyte1.08e-8072
stuff accumulating cell1.22e-6287
nongranular leukocyte9.56e-55115
myeloid cell5.38e-52108
common myeloid progenitor5.38e-52108
leukocyte3.18e-48136
hematopoietic lineage restricted progenitor cell3.54e-46120
hematopoietic stem cell6.90e-38168
angioblastic mesenchymal cell6.90e-38168
hematopoietic cell1.20e-35177
hematopoietic oligopotent progenitor cell3.87e-35161
hematopoietic multipotent progenitor cell3.87e-35161
mesenchymal cell1.33e-14354
connective tissue cell3.44e-14361
motile cell9.76e-13386
multi fate stem cell5.87e-11427
somatic stem cell1.03e-10433
stem cell2.15e-10441
single nucleate cell9.26e-083
mononuclear cell9.26e-083
Uber Anatomy
Ontology termp-valuen
bone marrow1.42e-7176
bone element5.88e-6682
hematopoietic system1.81e-6198
blood island1.81e-6198
skeletal element1.28e-5990
immune system1.62e-5793
hemolymphoid system2.96e-55108
skeletal system4.20e-53100
musculoskeletal system1.99e-29167
lateral plate mesoderm1.48e-26203
mesoderm8.03e-15315
mesoderm-derived structure8.03e-15315
presumptive mesoderm8.03e-15315
connective tissue1.26e-13371


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)
MA0003.12.72905e-14
MA0004.10.0184668
MA0006.10.0160925
MA0007.10.0154652
MA0009.10.212999
MA0014.17.65854e-09
MA0017.10.760848
MA0019.11.19317
MA0024.10.150131
MA0025.10.823085
MA0027.11.6684
MA0028.10.144668
MA0029.10.161009
MA0030.11.46475
MA0031.10.766324
MA0038.10.161161
MA0040.12.17832
MA0041.10.0950971
MA0042.10.193092
MA0043.10.213202
MA0046.10.594332
MA0048.10.122591
MA0050.10.194227
MA0051.10.157417
MA0052.10.498991
MA0055.10.0147252
MA0056.10
MA0057.10.00274634
MA0058.10.00656227
MA0059.10.00645491
MA0060.10.000208656
MA0061.10.0136793
MA0063.10
MA0066.10.161542
MA0067.10.4486
MA0068.10.284316
MA0069.10.588518
MA0070.10.571737
MA0071.10.30415
MA0072.10.193792
MA0073.156.7161
MA0074.10.156755
MA0076.10.117728
MA0077.10.189042
MA0078.10.927119
MA0081.10.0348384
MA0083.10.217849
MA0084.10.6087
MA0087.10.561402
MA0088.10.000692932
MA0089.10
MA0090.10.272498
MA0091.10.674691
MA0092.10.166183
MA0093.10.0027172
MA0095.10
MA0098.10
MA0100.10.0456513
MA0101.10.131708
MA0103.10.112297
MA0105.10.000457953
MA0106.10.0542605
MA0107.10.0550249
MA0108.22.44919
MA0109.10
MA0111.10.147308
MA0113.10.2165
MA0114.10.323021
MA0115.11.00523
MA0116.10.00574254
MA0117.10.668877
MA0119.10.087219
MA0122.10.255297
MA0124.10.934011
MA0125.10.291999
MA0130.10
MA0131.10.0808893
MA0132.10
MA0133.10
MA0135.11.22541
MA0136.10.38035
MA0139.10.00301568
MA0140.10.0308744
MA0141.10.0997393
MA0142.10.696374
MA0143.10.216681
MA0144.10.0147327
MA0145.19.56752e-05
MA0146.11.05037e-05
MA0147.10.00612796
MA0148.10.462701
MA0149.10.0286403
MA0062.20.0309256
MA0035.20.549044
MA0039.27.83154e-12
MA0138.20.257603
MA0002.20.0932517
MA0137.20.0216886
MA0104.20.000204242
MA0047.20.41952
MA0112.26.47023e-05
MA0065.20.0188846
MA0150.10.0452139
MA0151.10
MA0152.10.896147
MA0153.11.40073
MA0154.10.000406519
MA0155.10.00064931
MA0156.10.470033
MA0157.10.637835
MA0158.10
MA0159.10.0233099
MA0160.10.267542
MA0161.10
MA0162.12.08474e-07
MA0163.11.42172e-06
MA0164.10.0642528
MA0080.20.242062
MA0018.20.0547185
MA0099.20.310947
MA0079.20
MA0102.20.641748
MA0258.10.0123158
MA0259.10.00100083
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

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