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Coexpression cluster:C641: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.208137,0.506671,0.202418,0.857723,0.981802,0.319017,0.385011,0.628761,0.621506,0.968363,0.293498,1.08499,0.0649383,0.37489,0.169864,0.187326,0.587543,0.131867,0.534957,0.246002,0.202464,0.779448,0.312425,0.167123,0.238419,0.443987,0.20034,0.310589,0.173154,0.399779,0.275306,0.622056,0.355848,0.868889,0.447686,1.21188,0.143715,0.320003,0.401103,1.4408,0.445225,0.261903,1.5935,0.16875,0.111026,0.226447,0.385972,0.284438,0.312409,0.173249,0.456831,0.396393,0.873179,0.694739,0.841347,0.377467,1.00426,0.348876,0.399478,0.348003,0.660716,0.388062,0.299793,0.561703,0.403967,0.529794,0.927044,1.28869,0.612294,1.12869,0.700198,1.07567,0.123677,0.839414,0.0625815,0.205774,0.186653,0.546008,0.609242,0.659074,0.258113,0.560705,0.403653,0.307716,0.789807,0.268154,0.0982734,0.687175,0.480498,1.38705,1.01818,0.763867,0.637885,0.368116,0.171417,1.27368,0.53079,0.67819,0.484706,0.0378976,0.803034,0.632556,0.672898,0.590971,0.519171,0.289709,0.576179,0.371864,0.238217,0.15924,0.606372,0.670274,0.198172,0.301413,0.971251,0.439271,0.180319,0.274314,0.527634,0.116746,0.831412,0.478284,0.316671,0.413695,1.0796,0.546713,0.379419,0.642598,0.872646,0.784076,0.76453,0.277675,0.886589,0.410725,1.03079,0.161675,0.744364,0.836727,0.989273,1.83943,1.43902,0.95284,0.38094,0.674844,0.52079,0.341558,0.505455,1.68078,0.718674,0.112739,0.26835,0.0123511,0.764896,0.286124,0.387634,1.15881,0.465765,0.160686,0.670668,0.21563,0.951654,0.747146,1.47901,0.21815,0.535644,0.402951,0.10496,1.76904,0.570123
|tfbs_overrepresentation_jaspar=MA0003.1;0.000247383,MA0004.1;0.297884,MA0006.1;0.169524,MA0007.1;0.282081,MA0009.1;0.724811,MA0014.1;0.0237853,MA0017.1;0.57848,MA0019.1;0.428118,MA0024.1;0.6245,MA0025.1;0.854131,MA0027.1;2.32165,MA0028.1;0.181601,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;0.286538,MA0043.1;0.725115,MA0046.1;0.714324,MA0048.1;1.73714,MA0050.1;0.782956,MA0051.1;0.997995,MA0052.1;0.652145,MA0055.1;0.77794,MA0056.1;0,MA0057.1;0.294933,MA0058.1;0.219229,MA0059.1;0.218203,MA0060.1;0.0892161,MA0061.1;0.255087,MA0063.1;0,MA0066.1;0.387854,MA0067.1;1.03434,MA0068.1;0.196125,MA0069.1;0.710614,MA0070.1;0.69985,MA0071.1;0.35315,MA0072.1;0.695528,MA0073.1;0.056479,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;0.0644248,MA0089.1;0,MA0090.1;0.243681,MA0091.1;0.30011,MA0092.1;0.739628,MA0093.1;0.171791,MA0095.1;0,MA0098.1;0,MA0100.1;0.399896,MA0101.1;0.17426,MA0103.1;0.162663,MA0105.1;0.10818,MA0106.1;0.424592,MA0107.1;0.121572,MA0108.2;1.39378,MA0109.1;0,MA0111.1;0.708492,MA0113.1;0.439505,MA0114.1;0.376635,MA0115.1;0.959312,MA0116.1;1.27593,MA0117.1;0.76111,MA0119.1;0.205526,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;0.0663461,MA0140.1;0.350813,MA0141.1;0.216821,MA0142.1;0.541045,MA0143.1;0.439666,MA0144.1;0.35188,MA0145.1;0.194261,MA0146.1;0.0179216,MA0147.1;0.126316,MA0148.1;0.855011,MA0149.1;0.342334,MA0062.2;0.0702147,MA0035.2;0.350194,MA0039.2;0.14218,MA0138.2;1.19549,MA0002.2;0.280231,MA0137.2;0.54754,MA0104.2;0.088751,MA0047.2;0.413608,MA0112.2;0.592222,MA0065.2;0.388593,MA0150.1;0.238884,MA0151.1;0,MA0152.1;0.356591,MA0153.1;0.820317,MA0154.1;1.13157,MA0155.1;0.167839,MA0156.1;0.551743,MA0157.1;0.515488,MA0158.1;0,MA0159.1;0.126752,MA0160.1;0.332385,MA0161.1;0,MA0162.1;0.0446668,MA0163.1;0.02611,MA0164.1;0.450848,MA0080.2;1.56667,MA0018.2;0.425847,MA0099.2;0.938958,MA0079.2;0.022543,MA0102.2;1.25596,MA0258.1;1.13482,MA0259.1;0.412624,MA0442.1;0
}}
}}

Revision as of 19:20, 22 January 2013


Full id: C641_CD14_Neutrophils_Peripheral_Basophils_Whole_Monocytederived_Eosinophils



Phase1 CAGE Peaks

Hg19::chr10:106009594..106009596,+p@chr10:106009594..106009596
+
Hg19::chr11:6061520..6061539,+p@chr11:6061520..6061539
+
Hg19::chr17:4641746..4641758,-p@chr17:4641746..4641758
-
Hg19::chr17:57870810..57870824,+p@chr17:57870810..57870824
+
Hg19::chr19:52264235..52264246,+p6@FPR2
Hg19::chr1:153347033..153347045,-p3@S100A12
Hg19::chr21:39627657..39627671,+p@chr21:39627657..39627671
+
Hg19::chr21:39627673..39627684,+p@chr21:39627673..39627684
+
Hg19::chr2:132275749..132275752,+p@chr2:132275749..132275752
+
Hg19::chr3:194131791..194131795,-p@chr3:194131791..194131795
-
Hg19::chr6:31238972..31238985,-p12@HLA-C
Hg19::chr6:41196052..41196063,+p3@TREML4
Hg19::chr6:41196079..41196088,+p2@TREML4


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:0050832defense response to fungus0.0259961596961002
GO:0009620response to fungus0.0259961596961002
GO:0005626insoluble fraction0.0259961596961002
GO:0006805xenobiotic metabolic process0.0259961596961002
GO:0032393MHC class I receptor activity0.0259961596961002
GO:0009410response to xenobiotic stimulus0.0259961596961002
GO:0042742defense response to bacterium0.048525083909223
GO:0002474antigen processing and presentation of peptide antigen via MHC class I0.048525083909223
GO:0048002antigen processing and presentation of peptide antigen0.048525083909223
GO:0009617response to bacterium0.048525083909223



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 monocyte1.37e-12542
CD14-positive, CD16-negative classical monocyte1.37e-12542
defensive cell2.97e-10948
phagocyte2.97e-10948
monopoietic cell2.26e-8659
monocyte2.26e-8659
monoblast2.26e-8659
promonocyte2.26e-8659
macrophage dendritic cell progenitor2.03e-8361
myeloid lineage restricted progenitor cell8.33e-7766
granulocyte monocyte progenitor cell1.34e-7567
myeloid leukocyte3.43e-7572
stuff accumulating cell6.04e-5887
myeloid cell1.32e-48108
common myeloid progenitor1.32e-48108
nongranular leukocyte3.39e-45115
leukocyte2.91e-40136
hematopoietic lineage restricted progenitor cell3.61e-40120
hematopoietic stem cell1.32e-31168
angioblastic mesenchymal cell1.32e-31168
hematopoietic oligopotent progenitor cell6.23e-31161
hematopoietic multipotent progenitor cell6.23e-31161
hematopoietic cell9.95e-30177
mesenchymal cell4.40e-12354
connective tissue cell9.75e-12361
motile cell1.62e-10386
multi fate stem cell5.07e-09427
somatic stem cell8.16e-09433
stem cell1.51e-08441
Uber Anatomy
Ontology termp-valuen
bone marrow3.74e-6676
bone element5.43e-6182
skeletal element3.63e-5590
hematopoietic system7.09e-5498
blood island7.09e-5498
immune system3.09e-5393
skeletal system3.52e-49100
hemolymphoid system1.92e-48108
musculoskeletal system2.03e-27167
lateral plate mesoderm2.42e-23203
mesoderm3.16e-14315
mesoderm-derived structure3.16e-14315
presumptive mesoderm3.16e-14315
connective tissue2.89e-11371
dura mater4.90e-071
future meninx4.90e-071
ectomeninx4.90e-071
future dura mater4.90e-071


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)
MA0003.10.000247383
MA0004.10.297884
MA0006.10.169524
MA0007.10.282081
MA0009.10.724811
MA0014.10.0237853
MA0017.10.57848
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.181601
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.10.387473
MA0040.10.648455
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.11.73714
MA0050.10.782956
MA0051.10.997995
MA0052.10.652145
MA0055.10.77794
MA0056.10
MA0057.10.294933
MA0058.10.219229
MA0059.10.218203
MA0060.10.0892161
MA0061.10.255087
MA0063.10
MA0066.10.387854
MA0067.11.03434
MA0068.10.196125
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.10.695528
MA0073.10.056479
MA0074.10.383033
MA0076.10.231962
MA0077.10.688123
MA0078.10.473657
MA0081.10.623454
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.0644248
MA0089.10
MA0090.10.243681
MA0091.10.30011
MA0092.10.739628
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.17426
MA0103.10.162663
MA0105.10.10818
MA0106.10.424592
MA0107.10.121572
MA0108.21.39378
MA0109.10
MA0111.10.708492
MA0113.10.439505
MA0114.10.376635
MA0115.10.959312
MA0116.11.27593
MA0117.10.76111
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.10.0663461
MA0140.10.350813
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.10.35188
MA0145.10.194261
MA0146.10.0179216
MA0147.10.126316
MA0148.10.855011
MA0149.10.342334
MA0062.20.0702147
MA0035.20.350194
MA0039.20.14218
MA0138.21.19549
MA0002.20.280231
MA0137.20.54754
MA0104.20.088751
MA0047.20.413608
MA0112.20.592222
MA0065.20.388593
MA0150.10.238884
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.11.13157
MA0155.10.167839
MA0156.10.551743
MA0157.10.515488
MA0158.10
MA0159.10.126752
MA0160.10.332385
MA0161.10
MA0162.10.0446668
MA0163.10.02611
MA0164.10.450848
MA0080.21.56667
MA0018.20.425847
MA0099.20.938958
MA0079.20.022543
MA0102.21.25596
MA0258.11.13482
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

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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