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Coexpression cluster:C646: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.599307,0.0988421,0.585688,0.320418,0.17087,0.319017,1.00086,0.0904943,0.298989,0.0427817,0.797059,0.423573,0.859378,0.37489,0.169864,0.187326,0.587543,0.817657,0.250662,0.246002,0.202464,0.300734,0.312425,0.167123,1.24647,2.93696,0.0543847,0.310589,0.515041,0.399779,1.38383,0.622056,1.18646,0.506197,0.447686,0.681555,0.442053,0.320003,0.127608,0.570628,0.445225,0.724931,0.571235,0.16875,0.111026,1.20095,1.00297,1.41723,0.155427,0.173249,1.15689,1.02579,0.300076,0.694739,0.841347,0.984299,0.176395,0.348876,0.0468732,0.348003,0.660716,0.388062,0.0892869,0.561703,1.04233,1.31289,0.927044,1.28869,0.612294,1.12869,0.700198,1.07567,0.294551,0.839414,0.487306,1.20069,0.186653,0.546008,0.609242,0.233499,0.074278,0.560705,0.403653,0.0921949,0.789807,0.4388,1.48951,0.170958,0.480498,1.38705,1.01818,0.763867,0.637885,0.114875,0.171417,0.123575,1.36078,1.62465,1.21675,0.149342,0.12852,0.632556,0.672898,0.590971,0.519171,0.289709,1.41102,0.371864,0.670087,0.933941,1.14185,0.670274,0.575539,0.301413,0.971251,0.142611,0.180319,0.753394,0.527634,0.750778,0.831412,0.478284,0.316671,0.413695,1.0796,0.546713,0.988587,0.642598,0.872646,0.784076,0.76453,0.277675,0.886589,0.410725,1.03079,0.0417786,0.270369,0.836727,0.989273,1.83943,1.43902,0.95284,0.38094,0.674844,2.22958,0.341558,0.505455,1.68078,0.259186,0.732681,0.26835,0.159485,0.764896,0.286124,0.387634,1.15881,0.465765,0.48439,0.670668,0.617071,0.951654,0.747146,0.608503,0.21815,0.535644,0.402951,0.69704,0.383837,0.0488937
|tfbs_overrepresentation_for_novel_motifs=0.599307,0.0988421,0.585688,0.320418,0.17087,0.319017,1.00086,0.0904943,0.298989,0.0427817,0.797059,0.423573,0.859378,0.37489,0.169864,0.187326,0.587543,0.817657,0.250662,0.246002,0.202464,0.300734,0.312425,0.167123,1.24647,2.93696,0.0543847,0.310589,0.515041,0.399779,1.38383,0.622056,1.18646,0.506197,0.447686,0.681555,0.442053,0.320003,0.127608,0.570628,0.445225,0.724931,0.571235,0.16875,0.111026,1.20095,1.00297,1.41723,0.155427,0.173249,1.15689,1.02579,0.300076,0.694739,0.841347,0.984299,0.176395,0.348876,0.0468732,0.348003,0.660716,0.388062,0.0892869,0.561703,1.04233,1.31289,0.927044,1.28869,0.612294,1.12869,0.700198,1.07567,0.294551,0.839414,0.487306,1.20069,0.186653,0.546008,0.609242,0.233499,0.074278,0.560705,0.403653,0.0921949,0.789807,0.4388,1.48951,0.170958,0.480498,1.38705,1.01818,0.763867,0.637885,0.114875,0.171417,0.123575,1.36078,1.62465,1.21675,0.149342,0.12852,0.632556,0.672898,0.590971,0.519171,0.289709,1.41102,0.371864,0.670087,0.933941,1.14185,0.670274,0.575539,0.301413,0.971251,0.142611,0.180319,0.753394,0.527634,0.750778,0.831412,0.478284,0.316671,0.413695,1.0796,0.546713,0.988587,0.642598,0.872646,0.784076,0.76453,0.277675,0.886589,0.410725,1.03079,0.0417786,0.270369,0.836727,0.989273,1.83943,1.43902,0.95284,0.38094,0.674844,2.22958,0.341558,0.505455,1.68078,0.259186,0.732681,0.26835,0.159485,0.764896,0.286124,0.387634,1.15881,0.465765,0.48439,0.670668,0.617071,0.951654,0.747146,0.608503,0.21815,0.535644,0.402951,0.69704,0.383837,0.0488937
|tfbs_overrepresentation_jaspar=MA0003.1;0.0652591,MA0004.1;0.297884,MA0006.1;0.506155,MA0007.1;0.771118,MA0009.1;0.724811,MA0014.1;0.369455,MA0017.1;0.199401,MA0019.1;0.428118,MA0024.1;0.6245,MA0025.1;0.854131,MA0027.1;2.32165,MA0028.1;1.02527,MA0029.1;0.642879,MA0030.1;0.63197,MA0031.1;1.39986,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;0.287284,MA0051.1;0.383704,MA0052.1;0.652145,MA0055.1;0.083823,MA0056.1;0,MA0057.1;2.17648,MA0058.1;0.625569,MA0059.1;0.218203,MA0060.1;0.622587,MA0061.1;1.91627,MA0063.1;0,MA0066.1;0.387854,MA0067.1;1.03434,MA0068.1;0.760324,MA0069.1;0.710614,MA0070.1;2.80746,MA0071.1;0.35315,MA0072.1;0.695528,MA0073.1;0.983715,MA0074.1;0.383033,MA0076.1;1.22198,MA0077.1;0.688123,MA0078.1;0.473657,MA0081.1;0.218332,MA0083.1;0.732051,MA0084.1;1.21913,MA0087.1;0.693179,MA0088.1;0.854057,MA0089.1;0,MA0090.1;0.243681,MA0091.1;0.30011,MA0092.1;0.268302,MA0093.1;0.511707,MA0095.1;0,MA0098.1;0,MA0100.1;0.399896,MA0101.1;0.17426,MA0103.1;0.162663,MA0105.1;1.15008,MA0106.1;0.424592,MA0107.1;0.77236,MA0108.2;0.568002,MA0109.1;0,MA0111.1;1.30787,MA0113.1;0.439505,MA0114.1;0.118142,MA0115.1;0.959312,MA0116.1;0.123927,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;1.22896,MA0132.1;0,MA0133.1;0,MA0135.1;0.754112,MA0136.1;1.02008,MA0139.1;0.235473,MA0140.1;0.350813,MA0141.1;0.216821,MA0142.1;0.541045,MA0143.1;0.439666,MA0144.1;0.35188,MA0145.1;0.0753792,MA0146.1;0.886077,MA0147.1;0.397782,MA0148.1;0.319209,MA0149.1;0.342334,MA0062.2;1.35421,MA0035.2;0.350194,MA0039.2;1.01865,MA0138.2;0.474787,MA0002.2;0.280231,MA0137.2;0.186529,MA0104.2;0.298328,MA0047.2;0.413608,MA0112.2;0.0147485,MA0065.2;0.953721,MA0150.1;0.238884,MA0151.1;0,MA0152.1;0.356591,MA0153.1;0.820317,MA0154.1;0.105196,MA0155.1;1.18433,MA0156.1;1.05198,MA0157.1;0.515488,MA0158.1;0,MA0159.1;0.126752,MA0160.1;0.332385,MA0161.1;0,MA0162.1;1.33143,MA0163.1;1.65684,MA0164.1;0.450848,MA0080.2;0.511865,MA0018.2;0.425847,MA0099.2;0.356906,MA0079.2;7.59016,MA0102.2;1.25596,MA0258.1;0.102521,MA0259.1;0.132107,MA0442.1;0
}}
}}

Revision as of 19:20, 22 January 2013


Full id: C646_CD14_Mast_vagina_thymus_MCF7_immature_Eosinophils



Phase1 CAGE Peaks

Hg19::chr10:126847417..126847439,+p@chr10:126847417..126847439
+
Hg19::chr11:63953135..63953159,-p@chr11:63953135..63953159
-
Hg19::chr12:1704640..1704649,+p@chr12:1704640..1704649
+
Hg19::chr12:1704650..1704671,+p@chr12:1704650..1704671
+
Hg19::chr13:31191642..31191749,-p2@HMGB1
Hg19::chr6:31782588..31782612,+p@chr6:31782588..31782612
+
Hg19::chr6:31782632..31782654,+p@chr6:31782632..31782654
+
Hg19::chr6:31790025..31790063,+p@chr6:31790025..31790063
+
Hg19::chr6:44215668..44215690,+p13@HSP90AB1
Hg19::chr7:157129414..157129491,-p@chr7:157129414..157129491
-
Hg19::chr7:641637..641649,+p@chr7:641637..641649
+
Hg19::chr9:33025026..33025046,-p5@APTX
Hg19::chrX:118740549..118740569,+p@chrX:118740549..118740569
+


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:0006950response to stress0.00546884366603595
GO:0033699DNA 5'-adenosine monophosphate hydrolase activity0.00546884366603595
GO:0017055negative regulation of transcriptional preinitiation complex assembly0.00546884366603595
GO:00353125'-3' exodeoxyribonuclease activity0.00546884366603595
GO:0030911TPR domain binding0.00546884366603595
GO:0006288base-excision repair, DNA ligation0.00546884366603595
GO:0000785chromatin0.00546884366603595
GO:00084095'-3' exonuclease activity0.00546884366603595
GO:0030235nitric-oxide synthase regulator activity0.00546884366603595
GO:0008967phosphoglycolate phosphatase activity0.00546884366603595
GO:0006281DNA repair0.00546884366603595
GO:0000012single strand break repair0.00546884366603595
GO:0051103DNA ligation during DNA repair0.00546884366603595
GO:0006974response to DNA damage stimulus0.00546884366603595
GO:0051123transcriptional preinitiation complex assembly0.00546884366603595
GO:0045898regulation of transcriptional preinitiation complex assembly0.00546884366603595
GO:0044427chromosomal part0.00546884366603595
GO:0016895exodeoxyribonuclease activity, producing 5'-phosphomonoesters0.00561185847523729
GO:0004529exodeoxyribonuclease activity0.00561185847523729
GO:0045429positive regulation of nitric oxide biosynthetic process0.00561185847523729
GO:0009719response to endogenous stimulus0.00561185847523729
GO:0005694chromosome0.00561185847523729
GO:0006266DNA ligation0.00580392531463132
GO:0045428regulation of nitric oxide biosynthetic process0.00598028115587165
GO:0042221response to chemical stimulus0.00598028115587165
GO:0008301DNA bending activity0.00627481473872941
GO:0006268DNA unwinding during replication0.00878767242417505
GO:0032392DNA geometric change0.00920378733858085
GO:0032508DNA duplex unwinding0.00920378733858085
GO:0042542response to hydrogen peroxide0.00959366799323775
GO:0031647regulation of protein stability0.00959366799323775
GO:0046209nitric oxide metabolic process0.00959366799323775
GO:0016796exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.00959366799323775
GO:0006809nitric oxide biosynthetic process0.00959366799323775
GO:0008219cell death0.00981296665538481
GO:0016265death0.00981296665538481
GO:0000302response to reactive oxygen species0.0108178019051623
GO:0006284base-excision repair0.0136508321545364
GO:0047485protein N-terminus binding0.0148191578271127
GO:0048468cell development0.0161969686070464
GO:0006259DNA metabolic process0.0161969686070464
GO:0003684damaged DNA binding0.0172259976547266
GO:0004536deoxyribonuclease activity0.0172259976547266
GO:0000793condensed chromosome0.0174464800683915
GO:0003725double-stranded RNA binding0.0174464800683915
GO:0051789response to protein stimulus0.0185918184031567
GO:0006986response to unfolded protein0.0185918184031567
GO:0009891positive regulation of biosynthetic process0.0215915490740713
GO:0004527exonuclease activity0.0217539351273584
GO:0048770pigment granule0.0240862170172025
GO:0042470melanosome0.0240862170172025
GO:0065007biological regulation0.0251203755349182
GO:0048869cellular developmental process0.0255408107288152
GO:0030154cell differentiation0.0255408107288152
GO:0003690double-stranded DNA binding0.0290403494790685
GO:0003682chromatin binding0.0311238690921357
GO:0006979response to oxidative stress0.0311238690921357
GO:0019904protein domain specific binding0.0318162727159351
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0318162727159351
GO:0044271nitrogen compound biosynthetic process0.0361915885977443
GO:0043566structure-specific DNA binding0.0384906468708542
GO:0006261DNA-dependent DNA replication0.0386682473302357
GO:0005730nucleolus0.0386682473302357
GO:0006916anti-apoptosis0.0392117309418119
GO:0006310DNA recombination0.0433794383969251
GO:0043231intracellular membrane-bound organelle0.0433794383969251
GO:0043227membrane-bound organelle0.0433794383969251
GO:0051082unfolded protein binding0.0433794383969251
GO:0045892negative regulation of transcription, DNA-dependent0.0433881727652442
GO:0005515protein binding0.0446881835055404
GO:0009889regulation of biosynthetic process0.0450553585491057
GO:0043066negative regulation of apoptosis0.0464283747168019
GO:0043069negative regulation of programmed cell death0.0464283747168019
GO:0043232intracellular non-membrane-bound organelle0.0467892241541275
GO:0043228non-membrane-bound organelle0.0467892241541275
GO:0004518nuclease activity0.0476754711706606



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 monocyte4.76e-2742
CD14-positive, CD16-negative classical monocyte4.76e-2742
granulocyte monocyte progenitor cell1.61e-2567
defensive cell1.82e-2348
phagocyte1.82e-2348
myeloid lineage restricted progenitor cell2.94e-2366
macrophage dendritic cell progenitor3.50e-2361
myeloid leukocyte2.03e-2272
monopoietic cell1.55e-2159
monocyte1.55e-2159
monoblast1.55e-2159
promonocyte1.55e-2159
hematopoietic lineage restricted progenitor cell7.41e-16120
myeloid cell8.11e-16108
common myeloid progenitor8.11e-16108
leukocyte1.44e-14136
nongranular leukocyte4.53e-12115
hematopoietic oligopotent progenitor cell9.53e-12161
hematopoietic multipotent progenitor cell9.53e-12161
stuff accumulating cell3.06e-1187
hematopoietic stem cell4.20e-11168
angioblastic mesenchymal cell4.20e-11168
hematopoietic cell1.04e-10177
Uber Anatomy
Ontology termp-valuen
bone marrow5.28e-2376
bone element3.47e-2182
immune system8.22e-2093
hematopoietic system5.05e-1898
blood island5.05e-1898
skeletal element7.75e-1890
adult organism8.55e-18114
hemolymphoid system1.25e-15108
skeletal system1.79e-14100
neural tube4.76e-1456
neural rod4.76e-1456
future spinal cord4.76e-1456
neural keel4.76e-1456
regional part of nervous system4.08e-1353
regional part of brain4.08e-1353
regional part of forebrain5.32e-1041
forebrain5.32e-1041
anterior neural tube5.32e-1041
future forebrain5.32e-1041
brain3.30e-0968
future brain3.30e-0968
central nervous system9.78e-0981
neurectoderm4.52e-0886
neural plate1.10e-0782
presumptive neural plate1.10e-0782
brain grey matter1.44e-0734
gray matter1.44e-0734
telencephalon1.55e-0734
nervous system2.32e-0789
organ4.51e-07503


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)
MA0003.10.0652591
MA0004.10.297884
MA0006.10.506155
MA0007.10.771118
MA0009.10.724811
MA0014.10.369455
MA0017.10.199401
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.11.02527
MA0029.10.642879
MA0030.10.63197
MA0031.11.39986
MA0038.10.387473
MA0040.10.648455
MA0041.10.313738
MA0042.10.781261
MA0043.10.725115
MA0046.10.714324
MA0048.10.565955
MA0050.10.287284
MA0051.10.383704
MA0052.10.652145
MA0055.10.083823
MA0056.10
MA0057.12.17648
MA0058.10.625569
MA0059.10.218203
MA0060.10.622587
MA0061.11.91627
MA0063.10
MA0066.10.387854
MA0067.11.03434
MA0068.10.760324
MA0069.10.710614
MA0070.12.80746
MA0071.10.35315
MA0072.10.695528
MA0073.10.983715
MA0074.10.383033
MA0076.11.22198
MA0077.10.688123
MA0078.10.473657
MA0081.10.218332
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.854057
MA0089.10
MA0090.10.243681
MA0091.10.30011
MA0092.10.268302
MA0093.10.511707
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.17426
MA0103.10.162663
MA0105.11.15008
MA0106.10.424592
MA0107.10.77236
MA0108.20.568002
MA0109.10
MA0111.11.30787
MA0113.10.439505
MA0114.10.118142
MA0115.10.959312
MA0116.10.123927
MA0117.10.76111
MA0119.10.593096
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.11.22896
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.11.02008
MA0139.10.235473
MA0140.10.350813
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.10.35188
MA0145.10.0753792
MA0146.10.886077
MA0147.10.397782
MA0148.10.319209
MA0149.10.342334
MA0062.21.35421
MA0035.20.350194
MA0039.21.01865
MA0138.20.474787
MA0002.20.280231
MA0137.20.186529
MA0104.20.298328
MA0047.20.413608
MA0112.20.0147485
MA0065.20.953721
MA0150.10.238884
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.10.105196
MA0155.11.18433
MA0156.11.05198
MA0157.10.515488
MA0158.10
MA0159.10.126752
MA0160.10.332385
MA0161.10
MA0162.11.33143
MA0163.11.65684
MA0164.10.450848
MA0080.20.511865
MA0018.20.425847
MA0099.20.356906
MA0079.27.59016
MA0102.21.25596
MA0258.10.102521
MA0259.10.132107
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
CCNT2#905104.874001213048181.72226346360207e-066.49824688855263e-05
CHD2#110653.978470320814180.005583686566840480.0252524419241438
E2F6#187683.087480450275310.001215848534056670.00818288471764043
EGR1#195883.069648673729320.001265684169336790.00849202036241582
ELF1#199782.620367974650790.003725657351175790.0185765266924209
ELK4#200544.99559435645170.0065548508585910.0280176012450022
EP300#203363.126434642872250.006953716552815010.029409540903031
ETS1#211364.490197348708770.001065086822859670.00752412085312775
GTF2B#295949.828870749022840.0005466221481326220.00472041264501595
GTF2F1#296276.85981739517722.05623134739606e-050.000455269759785239
HEY1#2346292.796999952919340.0009141231142198250.00665296891470413
HSF1#3297788.46420512820515.05042282057528e-137.35650082228817e-11
IRF1#365974.112318944226720.0005475799661046840.00472751129040317
JUNB#372637.063992152266420.0077927501274330.0320167989991729
NFKB1#479072.955111074565910.00407132408296850.0194726605560152
PBX3#509046.742926980536660.002221995594476970.0127752820199054
POLR2A#5430132.147453176558074.83928878402115e-050.000840529654605662
PPARGC1A#108914107.7080419580424.61292015241441e-083.01482332789743e-06
SIN3A#2594283.328544447270850.0007191462059198680.00574519319208025
SRF#672255.30660702391070.001568264976097890.00994704395959477
STAT2#6773315.0608702737940.000916067850347980.00666572913136576
TAF1#687292.314416659362130.003942228691968590.0189515499360418
TAF7#687965.276801263811040.0004462923201972710.00415347742194642
TBP#690882.281089653597780.009285309085455830.0350760804273853
THAP1#5514537.239033369888770.007284337843234980.0301378188016329
WRNIP1#56897325.34306869600990.0002013293980992320.00239319838471269
YY1#752872.644476557613610.007760697146882240.0319177541672534



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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