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Coexpression cluster:C1286: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.0232809,0.384703,0.529489,0.343148,0.52784,0.604235,0.226729,0.224331,0.0544999,0.497563,0.647852,0.184039,1.44576,0.905441,0.365029,0.827563,0.28906,0.19568,0.0986842,1.77222,0.0646572,0.520063,1.60954,0.430372,0.670692,0.957451,1.28759,0.346214,0.150685,0.475674,0.864517,0.257226,0.186138,0.309012,0.021349,0.305874,0.529001,0.773034,0.207499,0.307642,0.459366,0.0729319,0.340293,0.0257952,1.06715,0.60533,0.486696,0.876276,0.915545,0.684981,0.617179,0.373994,0.941629,2.47889,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,1.87621,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,0.168304,0.156354,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.0324537,0.097572,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,2.06836,0.343884,0.277058,0.194299,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,3.22108,0.753567,0.493026,0.815341,0.589207,1.09919,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.039977,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.106334,0.0685123,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,1.81801,0.624608,0.24928,0.602897,0.00626991
|tfbs_overrepresentation_jaspar=MA0003.1;0.00215847,MA0004.1;4.33242,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.0156227,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;4.80736,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;9.7153,MA0042.1;6.6993,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.120314,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.0407081,MA0056.1;0,MA0057.1;0.115382,MA0058.1;4.85705,MA0059.1;1.84146,MA0060.1;0.224688,MA0061.1;0.575931,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.065183,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;2.81941,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.0723293,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;1.17914,MA0093.1;7.77568,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.104569,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;2.87791,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;1.491,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;1.04059,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.0807715,MA0146.1;0.0127148,MA0147.1;0.768766,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;5.86499,MA0035.2;0.564239,MA0039.2;0.00276064,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;1.85658,MA0047.2;0.636643,MA0112.2;0.0758925,MA0065.2;0.0828768,MA0150.1;1.92997,MA0151.1;0,MA0152.1;0.571637,MA0153.1;3.96897,MA0154.1;0.102476,MA0155.1;0.071478,MA0156.1;3.53048,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.0249953,MA0163.1;0.0167306,MA0164.1;0.678332,MA0080.2;5.472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.000432051,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:49, 22 January 2013


Full id: C1286_myelodysplastic_acute_leukemia_biphenotypic_CD14CD16_splenic_Dendritic



Phase1 CAGE Peaks

Hg19::chr8:130560794..130560810,-p@chr8:130560794..130560810
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Hg19::chr8:130560812..130560823,-p@chr8:130560812..130560823
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Hg19::chr8:130560843..130560854,-p@chr8:130560843..130560854
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Hg19::chr8:130560902..130560915,-p@chr8:130560902..130560915
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Hg19::chr8:130560925..130560948,-p@chr8:130560925..130560948
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Hg19::chr8:130560949..130560959,-p@chr8:130560949..130560959
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Hg19::chr8:27184282..27184305,+p6@PTK2B


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>disease_data<br>

Cell Type
Ontology termp-valuen
myeloid cell7.90e-33108
common myeloid progenitor7.90e-33108
hematopoietic oligopotent progenitor cell4.30e-28161
hematopoietic multipotent progenitor cell4.30e-28161
hematopoietic stem cell2.03e-26168
angioblastic mesenchymal cell2.03e-26168
macrophage dendritic cell progenitor1.77e-2461
hematopoietic cell1.83e-24177
monopoietic cell1.99e-2359
monocyte1.99e-2359
monoblast1.99e-2359
promonocyte1.99e-2359
granulocyte monocyte progenitor cell1.10e-2167
myeloid lineage restricted progenitor cell2.92e-2066
myeloid leukocyte1.10e-1972
classical monocyte1.78e-1942
CD14-positive, CD16-negative classical monocyte1.78e-1942
hematopoietic lineage restricted progenitor cell5.16e-17120
nongranular leukocyte8.18e-17115
defensive cell2.05e-1648
phagocyte2.05e-1648
intermediate monocyte2.76e-159
CD14-positive, CD16-positive monocyte2.76e-159
leukocyte4.11e-15136
non-classical monocyte7.33e-103
CD14-low, CD16-positive monocyte7.33e-103
immature conventional dendritic cell6.37e-085
common dendritic progenitor6.37e-085
stuff accumulating cell5.48e-0787
Uber Anatomy
Ontology termp-valuen
immune system4.46e-2193
hematopoietic system1.37e-1998
blood island1.37e-1998
bone marrow2.54e-1876
hemolymphoid system4.94e-17108
bone element1.71e-1682
skeletal element1.93e-1490
skeletal system2.41e-12100
hemopoietic organ4.60e-107
immune organ4.60e-107
spleen2.54e-093
gastrointestinal system mesentery2.54e-093
stomach region2.54e-093
mesentery2.54e-093
gastrointestinal system serosa2.54e-093
mesentery of stomach2.54e-093
gut mesentery2.54e-093
dorsal mesentery2.54e-093
dorsal mesogastrium2.54e-093
peritoneal cavity2.54e-093
spleen primordium2.54e-093
neural tube9.33e-0856
neural rod9.33e-0856
future spinal cord9.33e-0856
neural keel9.33e-0856
regional part of nervous system3.41e-0753
regional part of brain3.41e-0753
brainstem6.49e-076
basal ganglion6.63e-079
nuclear complex of neuraxis6.63e-079
aggregate regional part of brain6.63e-079
collection of basal ganglia6.63e-079
cerebral subcortex6.63e-079
neural nucleus6.91e-079
nucleus of brain6.91e-079
Disease
Ontology termp-valuen
myeloid leukemia8.41e-2231
leukemia3.40e-2139
hematologic cancer5.73e-1951
immune system cancer5.73e-1951


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)
MA0003.10.00215847
MA0004.14.33242
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.14.80736
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.19.7153
MA0042.16.6993
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.14.85705
MA0059.11.84146
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.065183
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.12.81941
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.11.17914
MA0093.17.77568
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.12.87791
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.11.491
MA0139.10.186511
MA0140.10.564957
MA0141.11.04059
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.0127148
MA0147.10.768766
MA0148.10.528066
MA0149.10.555119
MA0062.25.86499
MA0035.20.564239
MA0039.20.00276064
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.21.85658
MA0047.20.636643
MA0112.20.0758925
MA0065.20.0828768
MA0150.11.92997
MA0151.10
MA0152.10.571637
MA0153.13.96897
MA0154.10.102476
MA0155.10.071478
MA0156.13.53048
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.10.678332
MA0080.25.472
MA0018.20.650405
MA0099.20.572
MA0079.20.000432051
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
BATF#10538620.87811582197453.22775058778003e-082.17345611629374e-06
BCL11A#53335624.31667580309181.29931738009616e-089.61043965013196e-07
EBF1#187978.9064668465692.2473547136215e-071.19324595290247e-05
IRF4#3662412.52257867813950.0001356731131035550.00177719356069513
MEF2A#4205410.71041766265370.0002487360970091120.00268309742155904
NFKB1#479075.488063424193846.66568321176054e-060.000195002041723546
PAX5#507965.716770455295286.92762487228137e-050.00109956567482704
POU2F2#545267.805249192350731.11144903558223e-050.000284715785693336
RXRA#625638.603407345342830.003716461561497260.0187409361702097
SRF#6722611.82615279614389.50741412579311e-074.0677788770328e-05
USF1#739165.452713666178259.13505145927422e-050.00133173595666547
USF2#7392611.13616918720251.35815928956223e-065.33853210547948e-05
YY1#752864.209574928446160.000411683378865750.0039233324578301



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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