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Coexpression cluster:C469: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.102469,0.0577783,0.0984893,0.54841,0.266493,0.545716,0.239567,0.295736,0.290667,0.00531327,0.165709,0.272066,0.0823092,0.231159,0.560218,0.0881735,0.416635,0.760183,0.0930871,0.0677633,0.666991,0.151153,0.180548,0.259643,0.392149,0.289541,0.574586,0.179098,0.0787487,0.147924,0.462061,0.448071,0.157997,0.21322,0.0614574,0.095179,0.0600845,0.186559,0.420263,0.104553,1.25325,0.436576,0.941543,0.556551,0.00386387,0.115453,0.240368,0.158699,0.632018,0.078811,0.300624,0.249086,0.0936711,0.515129,0.653159,0.233295,0.581687,0.209799,0.147749,0.209089,0.483605,0.242112,0.122235,0.393294,0.255455,0.364726,0.73513,1.08739,1.11874,0.930562,0.133532,0.562687,0.00553467,0.651319,0.017273,0.0686019,0.157868,0.379205,0.436366,0.767791,0.737888,0.392395,0.709459,0.876309,0.604277,0.00144418,0.00355274,0.140525,0.321213,1.18432,0.823081,0.579812,0.462581,0.166137,0.0776122,0.406805,0.229209,0.499768,0.324895,0.42824,0.743127,0.45769,0.494867,0.419744,0.355282,0.16277,0.406348,0.228655,0.123981,0.0697646,0.104554,0.492438,0.0955593,0.171884,0.777703,0.47017,0.000295464,0.15094,0.951991,0.682586,1.55274,0.319278,0.183912,0.263675,0.882719,0.989505,0.234914,0.466912,0.683004,0.408938,0.580435,0.153507,0.696335,0.723221,0.835304,0.268768,0.147939,0.530448,0.795107,1.6331,1.23566,0.759951,0.236178,0.496668,0.356718,0.20386,0.908437,1.4753,0.43142,0.0420132,0.0781321,0.00135206,0.58078,0.113903,0.241755,0.959994,0.308372,0.247915,0.392237,0.107739,0.758809,0.564094,1.11126,0.354071,0.967734,0.708093,0.0377709,0.238589,0.00196777
|tfbs_overrepresentation_for_novel_motifs=0.102469,0.0577783,0.0984893,0.54841,0.266493,0.545716,0.239567,0.295736,0.290667,0.00531327,0.165709,0.272066,0.0823092,0.231159,0.560218,0.0881735,0.416635,0.760183,0.0930871,0.0677633,0.666991,0.151153,0.180548,0.259643,0.392149,0.289541,0.574586,0.179098,0.0787487,0.147924,0.462061,0.448071,0.157997,0.21322,0.0614574,0.095179,0.0600845,0.186559,0.420263,0.104553,1.25325,0.436576,0.941543,0.556551,0.00386387,0.115453,0.240368,0.158699,0.632018,0.078811,0.300624,0.249086,0.0936711,0.515129,0.653159,0.233295,0.581687,0.209799,0.147749,0.209089,0.483605,0.242112,0.122235,0.393294,0.255455,0.364726,0.73513,1.08739,1.11874,0.930562,0.133532,0.562687,0.00553467,0.651319,0.017273,0.0686019,0.157868,0.379205,0.436366,0.767791,0.737888,0.392395,0.709459,0.876309,0.604277,0.00144418,0.00355274,0.140525,0.321213,1.18432,0.823081,0.579812,0.462581,0.166137,0.0776122,0.406805,0.229209,0.499768,0.324895,0.42824,0.743127,0.45769,0.494867,0.419744,0.355282,0.16277,0.406348,0.228655,0.123981,0.0697646,0.104554,0.492438,0.0955593,0.171884,0.777703,0.47017,0.000295464,0.15094,0.951991,0.682586,1.55274,0.319278,0.183912,0.263675,0.882719,0.989505,0.234914,0.466912,0.683004,0.408938,0.580435,0.153507,0.696335,0.723221,0.835304,0.268768,0.147939,0.530448,0.795107,1.6331,1.23566,0.759951,0.236178,0.496668,0.356718,0.20386,0.908437,1.4753,0.43142,0.0420132,0.0781321,0.00135206,0.58078,0.113903,0.241755,0.959994,0.308372,0.247915,0.392237,0.107739,0.758809,0.564094,1.11126,0.354071,0.967734,0.708093,0.0377709,0.238589,0.00196777
|tfbs_overrepresentation_jaspar=MA0003.1;4.3196e-05,MA0004.1;0.169125,MA0006.1;0.0763783,MA0007.1;0.156885,MA0009.1;0.543169,MA0014.1;1.91579e-05,MA0017.1;0.31911,MA0019.1;0.275941,MA0024.1;0.450307,MA0025.1;0.665335,MA0027.1;2.11401,MA0028.1;0.0843345,MA0029.1;0.467171,MA0030.1;0.457153,MA0031.1;1.03709,MA0038.1;0.678012,MA0040.1;0.472301,MA0041.1;0.181587,MA0042.1;0.160318,MA0043.1;0.543454,MA0046.1;1.32049,MA0048.1;0.00619675,MA0050.1;0.484906,MA0051.1;0.238478,MA0052.1;0.475699,MA0055.1;0.0108548,MA0056.1;0,MA0057.1;0.197491,MA0058.1;0.110291,MA0059.1;0.109562,MA0060.1;0.0296044,MA0061.1;0.237238,MA0063.1;0,MA0066.1;0.241938,MA0067.1;0.83875,MA0068.1;0.0636439,MA0069.1;1.31314,MA0070.1;0.519883,MA0071.1;2.53681,MA0072.1;2.21336,MA0073.1;5.64098e-06,MA0074.1;0.23792,MA0076.1;0.119431,MA0077.1;0.508982,MA0078.1;0.31524,MA0081.1;0.109654,MA0083.1;0.549943,MA0084.1;1.01907,MA0087.1;0.513678,MA0088.1;0.0105133,MA0089.1;0,MA0090.1;0.402075,MA0091.1;0.170864,MA0092.1;0.448732,MA0093.1;0.0778562,MA0095.1;0,MA0098.1;0,MA0100.1;0.252028,MA0101.1;0.574673,MA0103.1;0.251512,MA0105.1;0.0246233,MA0106.1;0.272934,MA0107.1;0.177872,MA0108.2;0.398967,MA0109.1;0,MA0111.1;0.423052,MA0113.1;0.285689,MA0114.1;0.17185,MA0115.1;0.766188,MA0116.1;0.182019,MA0117.1;0.577217,MA0119.1;0.100647,MA0122.1;0.600851,MA0124.1;0.727093,MA0125.1;1.56326,MA0130.1;0,MA0131.1;0.329895,MA0132.1;0,MA0133.1;0,MA0135.1;1.39934,MA0136.1;0.246897,MA0139.1;0.213944,MA0140.1;0.211376,MA0141.1;0.351584,MA0142.1;0.978356,MA0143.1;0.779645,MA0144.1;0.155387,MA0145.1;0.0458033,MA0146.1;0.0432698,MA0147.1;0.049714,MA0148.1;0.546085,MA0149.1;0.204488,MA0062.2;0.0907669,MA0035.2;0.210872,MA0039.2;0.00708527,MA0138.2;0.316226,MA0002.2;0.799796,MA0137.2;0.295276,MA0104.2;0.0293723,MA0047.2;0.263601,MA0112.2;0.00179367,MA0065.2;0.220145,MA0150.1;0.785204,MA0151.1;0,MA0152.1;0.618168,MA0153.1;0.633172,MA0154.1;0.299683,MA0155.1;0.0102223,MA0156.1;0.0888107,MA0157.1;0.928131,MA0158.1;0,MA0159.1;0.417407,MA0160.1;0.571442,MA0161.1;0,MA0162.1;0.0119377,MA0163.1;0.00138779,MA0164.1;0.801488,MA0080.2;0.0778984,MA0018.2;0.274004,MA0099.2;0.216352,MA0079.2;1.44559e-06,MA0102.2;1.05522,MA0258.1;0.0364681,MA0259.1;0.196503,MA0442.1;0
}}
}}

Revision as of 19:11, 22 January 2013


Full id: C469_Neutrophils_Monocytederived_CD14_CD19_Eosinophils_blood_Macrophage



Phase1 CAGE Peaks

Hg19::chr12:51636570..51636602,+p@chr12:51636570..51636602
+
Hg19::chr16:21652353..21652374,-p@chr16:21652353..21652374
-
Hg19::chr17:4621210..4621234,+p@chr17:4621210..4621234
+
Hg19::chr17:73316259..73316283,-p@chr17:73316259..73316283
-
Hg19::chr17:9818724..9818740,-p@chr17:9818724..9818740
-
Hg19::chr18:60241636..60241638,+p13@ZCCHC2
Hg19::chr1:111441802..111441817,+p@chr1:111441802..111441817
+
Hg19::chr1:150724282..150724308,-p8@CTSS
Hg19::chr1:31206348..31206387,-p@chr1:31206348..31206387
-
Hg19::chr1:31206388..31206521,-p@chr1:31206388..31206521
-
Hg19::chr21:46306100..46306113,-p@chr21:46306100..46306113
-
Hg19::chr2:109301897..109301905,+p1@uc002tel.2
Hg19::chr3:128533128..128533149,+p4@RAB7A
Hg19::chr3:69154031..69154043,+p@chr3:69154031..69154043
+
Hg19::chr5:179440262..179440275,-p6@RNF130
Hg19::chr7:26413020..26413035,+p@chr7:26413020..26413035
+
Hg19::chr7:99987647..99987671,+p@chr7:99987647..99987671
+
Hg19::chr8:17914448..17914471,-p@chr8:17914448..17914471
-
Hg19::chr8:38677993..38678006,+p17@TACC1
Hg19::chrX:119590605..119590629,-p@chrX:119590605..119590629
-
Hg19::chrX:37658283..37658294,+p@chrX:37658283..37658294
+


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:0004218cathepsin S activity0.01247560268708
GO:0005764lysosome0.01247560268708
GO:0000323lytic vacuole0.01247560268708
GO:0005773vacuole0.01247560268708



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
myeloid leukocyte3.12e-5672
monopoietic cell4.92e-5659
monocyte4.92e-5659
monoblast4.92e-5659
promonocyte4.92e-5659
macrophage dendritic cell progenitor7.93e-5661
defensive cell8.89e-5648
phagocyte8.89e-5648
granulocyte monocyte progenitor cell8.59e-5367
myeloid lineage restricted progenitor cell9.96e-5266
classical monocyte4.64e-4842
CD14-positive, CD16-negative classical monocyte4.64e-4842
myeloid cell1.82e-45108
common myeloid progenitor1.82e-45108
nongranular leukocyte1.42e-44115
leukocyte1.99e-44136
hematopoietic oligopotent progenitor cell1.51e-42161
hematopoietic multipotent progenitor cell1.51e-42161
hematopoietic stem cell4.62e-42168
angioblastic mesenchymal cell4.62e-42168
hematopoietic lineage restricted progenitor cell1.88e-41120
hematopoietic cell2.65e-38177
stuff accumulating cell1.13e-2587
mesenchymal cell5.94e-10354
connective tissue cell3.00e-09361
macrophage6.45e-096
intermediate monocyte7.44e-099
CD14-positive, CD16-positive monocyte7.44e-099
motile cell7.11e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.42e-4998
blood island3.42e-4998
hemolymphoid system1.78e-45108
bone marrow2.26e-4576
immune system3.53e-4193
bone element1.89e-4082
skeletal element6.17e-3590
skeletal system1.21e-31100
lateral plate mesoderm1.41e-14203
musculoskeletal system1.36e-11167
connective tissue1.10e-08371
adult organism2.37e-07114


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)
MA0003.14.3196e-05
MA0004.10.169125
MA0006.10.0763783
MA0007.10.156885
MA0009.10.543169
MA0014.11.91579e-05
MA0017.10.31911
MA0019.10.275941
MA0024.10.450307
MA0025.10.665335
MA0027.12.11401
MA0028.10.0843345
MA0029.10.467171
MA0030.10.457153
MA0031.11.03709
MA0038.10.678012
MA0040.10.472301
MA0041.10.181587
MA0042.10.160318
MA0043.10.543454
MA0046.11.32049
MA0048.10.00619675
MA0050.10.484906
MA0051.10.238478
MA0052.10.475699
MA0055.10.0108548
MA0056.10
MA0057.10.197491
MA0058.10.110291
MA0059.10.109562
MA0060.10.0296044
MA0061.10.237238
MA0063.10
MA0066.10.241938
MA0067.10.83875
MA0068.10.0636439
MA0069.11.31314
MA0070.10.519883
MA0071.12.53681
MA0072.12.21336
MA0073.15.64098e-06
MA0074.10.23792
MA0076.10.119431
MA0077.10.508982
MA0078.10.31524
MA0081.10.109654
MA0083.10.549943
MA0084.11.01907
MA0087.10.513678
MA0088.10.0105133
MA0089.10
MA0090.10.402075
MA0091.10.170864
MA0092.10.448732
MA0093.10.0778562
MA0095.10
MA0098.10
MA0100.10.252028
MA0101.10.574673
MA0103.10.251512
MA0105.10.0246233
MA0106.10.272934
MA0107.10.177872
MA0108.20.398967
MA0109.10
MA0111.10.423052
MA0113.10.285689
MA0114.10.17185
MA0115.10.766188
MA0116.10.182019
MA0117.10.577217
MA0119.10.100647
MA0122.10.600851
MA0124.10.727093
MA0125.11.56326
MA0130.10
MA0131.10.329895
MA0132.10
MA0133.10
MA0135.11.39934
MA0136.10.246897
MA0139.10.213944
MA0140.10.211376
MA0141.10.351584
MA0142.10.978356
MA0143.10.779645
MA0144.10.155387
MA0145.10.0458033
MA0146.10.0432698
MA0147.10.049714
MA0148.10.546085
MA0149.10.204488
MA0062.20.0907669
MA0035.20.210872
MA0039.20.00708527
MA0138.20.316226
MA0002.20.799796
MA0137.20.295276
MA0104.20.0293723
MA0047.20.263601
MA0112.20.00179367
MA0065.20.220145
MA0150.10.785204
MA0151.10
MA0152.10.618168
MA0153.10.633172
MA0154.10.299683
MA0155.10.0102223
MA0156.10.0888107
MA0157.10.928131
MA0158.10
MA0159.10.417407
MA0160.10.571442
MA0161.10
MA0162.10.0119377
MA0163.10.00138779
MA0164.10.801488
MA0080.20.0778984
MA0018.20.274004
MA0099.20.216352
MA0079.21.44559e-06
MA0102.21.05522
MA0258.10.0364681
MA0259.10.196503
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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