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Coexpression cluster:C654: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.208137,0.981855,0.202418,0.320418,0.17087,0.319017,0.385011,0.628761,1.04054,0.251333,0.293498,0.423573,0.499876,0.37489,0.506988,0.549464,0.587543,0.412009,0.250662,0.74987,0.202464,0.300734,0.312425,0.167123,0.238419,0.443987,0.772359,0.310589,0.173154,0.399779,0.755662,0.622056,0.721119,0.234859,0.145955,0.928315,0.442053,0.320003,0.127608,0.570628,0.144976,0.261903,0.340762,0.16875,0.360234,0.642555,0.385972,1.41723,0.312409,0.515273,0.456831,0.396393,0.551018,0.694739,0.841347,0.377467,0.176395,0.348876,0.706527,0.348003,0.660716,0.388062,0.62293,0.561703,0.403967,0.529794,0.927044,1.28869,0.612294,1.12869,0.700198,1.07567,0.294551,0.839414,0.224555,1.20069,0.186653,0.546008,0.609242,0.659074,0.548433,0.560705,0.403653,1.06327,0.789807,0.268154,0.0982734,0.687175,0.480498,1.38705,1.01818,0.763867,0.637885,0.114875,0.984035,0.123575,0.248364,0.67819,1.21675,0.972854,0.403442,0.632556,0.672898,0.590971,0.519171,0.289709,0.576179,0.371864,0.670087,0.15924,0.606372,0.670274,0.198172,0.814965,0.971251,0.439271,0.767357,0.753394,0.527634,0.116746,0.831412,0.478284,0.316671,0.413695,1.0796,0.546713,0.379419,0.642598,0.872646,0.124214,0.76453,0.277675,0.886589,1.86125,1.03079,1.02457,0.270369,0.836727,0.989273,1.83943,1.43902,0.95284,0.38094,0.674844,0.52079,0.341558,0.505455,1.68078,0.259186,0.362523,0.110712,0.159485,0.764896,0.0843101,0.387634,1.15881,0.465765,0.160686,0.238466,0.617071,0.951654,0.747146,0.608503,0.623024,0.535644,0.402951,0.341994,0.383837,1.23381
|tfbs_overrepresentation_jaspar=MA0003.1;1.11833,MA0004.1;0.806989,MA0006.1;0.506155,MA0007.1;0.282081,MA0009.1;0.724811,MA0014.1;0.369455,MA0017.1;1.09607,MA0019.1;0.428118,MA0024.1;0.6245,MA0025.1;0.854131,MA0027.1;2.32165,MA0028.1;0.535609,MA0029.1;0.642879,MA0030.1;0.63197,MA0031.1;0.570886,MA0038.1;0.387473,MA0040.1;0.648455,MA0041.1;0.313738,MA0042.1;0.781261,MA0043.1;0.725115,MA0046.1;0.714324,MA0048.1;0.565955,MA0050.1;1.4276,MA0051.1;0.997995,MA0052.1;0.652145,MA0055.1;2.63233,MA0056.1;0,MA0057.1;0.542827,MA0058.1;1.17324,MA0059.1;1.82562,MA0060.1;0.0892161,MA0061.1;1.91627,MA0063.1;0,MA0066.1;0.387854,MA0067.1;1.03434,MA0068.1;0.434546,MA0069.1;0.710614,MA0070.1;0.69985,MA0071.1;0.35315,MA0072.1;0.695528,MA0073.1;1.17639,MA0074.1;0.383033,MA0076.1;0.231962,MA0077.1;0.688123,MA0078.1;0.473657,MA0081.1;0.623454,MA0083.1;0.732051,MA0084.1;1.21913,MA0087.1;0.693179,MA0088.1;0.566948,MA0089.1;0,MA0090.1;1.26632,MA0091.1;0.30011,MA0092.1;0.268302,MA0093.1;0.985558,MA0095.1;0,MA0098.1;0,MA0100.1;0.399896,MA0101.1;1.58055,MA0103.1;0.489275,MA0105.1;2.55034,MA0106.1;0.424592,MA0107.1;1.83421,MA0108.2;0.568002,MA0109.1;0,MA0111.1;0.254772,MA0113.1;0.439505,MA0114.1;0.376635,MA0115.1;0.959312,MA0116.1;2.50474,MA0117.1;0.76111,MA0119.1;0.593096,MA0122.1;0.786181,MA0124.1;0.918678,MA0125.1;0.83671,MA0130.1;0,MA0131.1;0.490408,MA0132.1;0,MA0133.1;0,MA0135.1;0.754112,MA0136.1;0.393782,MA0139.1;0.870578,MA0140.1;0.350813,MA0141.1;0.216821,MA0142.1;0.541045,MA0143.1;0.439666,MA0144.1;0.714233,MA0145.1;0.626532,MA0146.1;0.191696,MA0147.1;0.397782,MA0148.1;0.319209,MA0149.1;0.342334,MA0062.2;0.900923,MA0035.2;0.350194,MA0039.2;0.465551,MA0138.2;0.474787,MA0002.2;0.99121,MA0137.2;1.04503,MA0104.2;0.620335,MA0047.2;0.413608,MA0112.2;0.0147485,MA0065.2;0.641236,MA0150.1;0.671641,MA0151.1;0,MA0152.1;0.356591,MA0153.1;0.820317,MA0154.1;0.7755,MA0155.1;0.333744,MA0156.1;0.551743,MA0157.1;1.28247,MA0158.1;0,MA0159.1;0.398903,MA0160.1;0.332385,MA0161.1;0,MA0162.1;0.107144,MA0163.1;3.23044,MA0164.1;0.450848,MA0080.2;0.985821,MA0018.2;0.425847,MA0099.2;0.356906,MA0079.2;1.62563,MA0102.2;1.25596,MA0258.1;0.102521,MA0259.1;0.412624,MA0442.1;0
}}
}}

Revision as of 19:20, 22 January 2013


Full id: C654_Eosinophils_Neutrophils_Natural_CD8_CD4_CD14_CD34



Phase1 CAGE Peaks

Hg19::chr11:269478..269491,-p@chr11:269478..269491
-
Hg19::chr17:40440375..40440398,-p@chr17:40440375..40440398
-
Hg19::chr17:47817223..47817245,+p@chr17:47817223..47817245
+
Hg19::chr17:7747301..7747312,-p@chr17:7747301..7747312
-
Hg19::chr19:13948014..13948028,+p@chr19:13948014..13948028
+
Hg19::chr2:43386231..43386235,+p@chr2:43386231..43386235
+
Hg19::chr2:70313762..70313774,-p18@PCBP1-AS1
Hg19::chr3:196438771..196438791,-p@chr3:196438771..196438791
-
Hg19::chr4:123073610..123073629,+p2@KIAA1109
Hg19::chr5:131763102..131763114,-p@chr5:131763102..131763114
-
Hg19::chr9:117135390..117135416,-p@chr9:117135390..117135416
-
Hg19::chr9:117145466..117145492,+p@chr9:117145466..117145492
+
Hg19::chr9:117147710..117147721,-p@chr9:117147710..117147721
-


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:0004190aspartic-type endopeptidase activity0.0275226657247145



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
leukocyte3.63e-67136
hematopoietic stem cell3.81e-52168
angioblastic mesenchymal cell3.81e-52168
hematopoietic lineage restricted progenitor cell4.68e-50120
hematopoietic cell5.15e-50177
nongranular leukocyte1.62e-49115
hematopoietic oligopotent progenitor cell7.12e-48161
hematopoietic multipotent progenitor cell7.12e-48161
myeloid leukocyte4.96e-3972
classical monocyte7.38e-3642
CD14-positive, CD16-negative classical monocyte7.38e-3642
defensive cell3.23e-3048
phagocyte3.23e-3048
granulocyte monocyte progenitor cell1.35e-2867
macrophage dendritic cell progenitor1.27e-2661
myeloid cell4.93e-26108
common myeloid progenitor4.93e-26108
myeloid lineage restricted progenitor cell1.77e-2566
mature alpha-beta T cell1.89e-2418
alpha-beta T cell1.89e-2418
immature T cell1.89e-2418
mature T cell1.89e-2418
immature alpha-beta T cell1.89e-2418
monopoietic cell4.74e-2459
monocyte4.74e-2459
monoblast4.74e-2459
promonocyte4.74e-2459
lymphoid lineage restricted progenitor cell1.39e-2052
lymphocyte4.77e-2053
common lymphoid progenitor4.77e-2053
nucleate cell4.90e-1955
T cell1.78e-1825
pro-T cell1.78e-1825
granulocyte3.82e-188
intermediate monocyte1.14e-169
CD14-positive, CD16-positive monocyte1.14e-169
blood cell1.45e-1511
CD8-positive, alpha-beta T cell1.56e-1411
mesenchymal cell2.34e-14354
connective tissue cell1.03e-13361
CD4-positive, alpha-beta T cell1.13e-136
stuff accumulating cell8.72e-1387
motile cell1.86e-11386
multi fate stem cell9.38e-09427
stem cell1.84e-08441
somatic stem cell2.18e-08433
neutrophil4.27e-083
natural killer cell4.36e-083
pro-NK cell4.36e-083
naive T cell1.49e-073
basophil1.81e-073
single nucleate cell2.15e-073
mononuclear cell2.15e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.40e-3898
blood island7.40e-3898
hemolymphoid system1.58e-34108
bone marrow5.26e-2476
immune system5.90e-2393
bone element1.64e-2182
skeletal element1.03e-1890
skeletal system7.29e-16100
blood8.10e-1515
haemolymphatic fluid8.10e-1515
organism substance8.10e-1515
connective tissue7.78e-13371
lateral plate mesoderm2.70e-11203


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)
MA0003.11.11833
MA0004.10.806989
MA0006.10.506155
MA0007.10.282081
MA0009.10.724811
MA0014.10.369455
MA0017.11.09607
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.535609
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.10.387473
MA0040.10.648455
MA0041.10.313738
MA0042.10.781261
MA0043.10.725115
MA0046.10.714324
MA0048.10.565955
MA0050.11.4276
MA0051.10.997995
MA0052.10.652145
MA0055.12.63233
MA0056.10
MA0057.10.542827
MA0058.11.17324
MA0059.11.82562
MA0060.10.0892161
MA0061.11.91627
MA0063.10
MA0066.10.387854
MA0067.11.03434
MA0068.10.434546
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.10.695528
MA0073.11.17639
MA0074.10.383033
MA0076.10.231962
MA0077.10.688123
MA0078.10.473657
MA0081.10.623454
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.566948
MA0089.10
MA0090.11.26632
MA0091.10.30011
MA0092.10.268302
MA0093.10.985558
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.11.58055
MA0103.10.489275
MA0105.12.55034
MA0106.10.424592
MA0107.11.83421
MA0108.20.568002
MA0109.10
MA0111.10.254772
MA0113.10.439505
MA0114.10.376635
MA0115.10.959312
MA0116.12.50474
MA0117.10.76111
MA0119.10.593096
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.10.870578
MA0140.10.350813
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.10.714233
MA0145.10.626532
MA0146.10.191696
MA0147.10.397782
MA0148.10.319209
MA0149.10.342334
MA0062.20.900923
MA0035.20.350194
MA0039.20.465551
MA0138.20.474787
MA0002.20.99121
MA0137.21.04503
MA0104.20.620335
MA0047.20.413608
MA0112.20.0147485
MA0065.20.641236
MA0150.10.671641
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.10.7755
MA0155.10.333744
MA0156.10.551743
MA0157.11.28247
MA0158.10
MA0159.10.398903
MA0160.10.332385
MA0161.10
MA0162.10.107144
MA0163.13.23044
MA0164.10.450848
MA0080.20.985821
MA0018.20.425847
MA0099.20.356906
MA0079.21.62563
MA0102.21.25596
MA0258.10.102521
MA0259.10.412624
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
BCL11A#53335613.09359466320332.65123192532282e-069.29167822311376e-05
CTCF#1066472.886291893194250.004675127804286980.022060528294941
EBF1#1879106.851128343514626.58271412928801e-084.02512927955919e-06
ELF1#199792.947913971482140.0006034034679179530.00503989561627344
GABPB1#255363.262007924391770.005616304413831570.0253944591166402
IRF4#366258.428658725670820.0001867922617576610.00225974713607186
MAX#414962.978102542618670.008858766958238280.0336155492624877
NFKB1#4790114.643745974317863.97495193507342e-071.92551022795516e-05
PAX5#507963.078261014389770.007515152955548730.0309884341252588
POLR2A#5430132.147453176558074.83928878402115e-050.000840809318440167
POU2F2#545253.502355406824050.009616138602656820.0361896832374644
SP1#666773.068359203614330.003260177412074160.0168860180886537
SPI1#668874.417712658435310.0003496087924691540.00352951113356076
SRF#672255.30660702391070.001568264976097890.00994764809223732
TAF1#6872102.571574065957920.0006350412348224820.0052112101456451
TBP#6908113.136498273696942.43452380190334e-050.000528166247085547
TCF12#693886.544286093653185.08413564000193e-060.000156724333561441
USF1#739162.93607658948060.009503763178720540.0358003073984633
USF2#739243.997599195406030.01425460739215360.049996203157777



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C654&oldid=2569165"