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Coexpression cluster:C866: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.312007,0.136365,0.305225,0.440628,0.737182,1.11855,0.511871,0.953643,0.487494,0.840518,0.410439,0.553754,0.127813,0.500805,0.266007,0.287179,0.728104,0.624077,0.137566,0.0599474,1.49268,0.940495,0.431698,0.262652,0.347482,0.575764,0.112018,0.429643,0.270022,0.329945,0.389837,0.764231,0.190489,0.807612,0.23642,0.261421,0.233607,0.440165,0.213144,0.451713,0.235191,0.374544,1.44736,0.731232,0.513344,0.333541,0.51292,0.4002,0.963411,0.270138,0.589559,0.524278,0.546719,0.839846,0.99088,0.503626,0.273964,0.472204,0.329728,0.47124,0.804523,0.5152,0.488493,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,0.0724994,0.988898,0.124338,0.367887,0.342172,0.684401,0.750836,0.341765,0.436045,0.699894,0.532172,0.166331,0.937974,0.0150019,0.0591186,0.320664,0.614883,1.54397,1.17124,0.911274,0.78075,0.196636,0.267904,1.12954,0.136404,0.82268,0.619373,0.0858425,0.214313,0.775192,1.91213,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.252953,0.315525,0.814459,0.300169,0.41935,1.12352,0.656078,0.0867932,0.388709,0.664981,0.199081,0.980696,0.612519,1.11289,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.600821,0.911957,0.39253,1.03718,0.539846,1.18405,0.636999,0.384215,1.09932,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,1.54804,1.83907,0.37143,0.193834,0.50389,0.0382049,0.912334,0.155464,0.514733,1.31376,0.599133,0.708413,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,0.540317,0.510589,0.731963
|tfbs_overrepresentation_jaspar=MA0003.1;0.0416606,MA0004.1;1.06719,MA0006.1;0.265592,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;0.367355,MA0017.1;0.815464,MA0019.1;0.558663,MA0024.1;0.766783,MA0025.1;1.00397,MA0027.1;2.48103,MA0028.1;0.280275,MA0029.1;0.785955,MA0030.1;0.774581,MA0031.1;0.710608,MA0038.1;1.28049,MA0040.1;0.791764,MA0041.1;0.433167,MA0042.1;0.402577,MA0043.1;0.871285,MA0046.1;0.860127,MA0048.1;1.41801,MA0050.1;0.403421,MA0051.1;0.510444,MA0052.1;0.795605,MA0055.1;1.02363,MA0056.1;0,MA0057.1;0.253359,MA0058.1;0.86817,MA0059.1;0.865474,MA0060.1;0.162248,MA0061.1;0.851955,MA0063.1;0,MA0066.1;0.514973,MA0067.1;1.18766,MA0068.1;0.354973,MA0069.1;0.856287,MA0070.1;0.845142,MA0071.1;0.47692,MA0072.1;0.840664,MA0073.1;0.447621,MA0074.1;0.509711,MA0076.1;0.339975,MA0077.1;0.832987,MA0078.1;0.607575,MA0081.1;0.324031,MA0083.1;2.03788,MA0084.1;1.37471,MA0087.1;0.838229,MA0088.1;0.650888,MA0089.1;0,MA0090.1;0.353576,MA0091.1;0.417885,MA0092.1;0.993944,MA0093.1;1.35827,MA0095.1;0,MA0098.1;0,MA0100.1;1.30927,MA0101.1;0.746654,MA0103.1;0.257174,MA0105.1;0.496814,MA0106.1;0.554855,MA0107.1;1.11943,MA0108.2;0.707575,MA0109.1;0,MA0111.1;0.366362,MA0113.1;0.57094,MA0114.1;0.582067,MA0115.1;1.11137,MA0116.1;1.13131,MA0117.1;0.908433,MA0119.1;0.308914,MA0122.1;0.934245,MA0124.1;1.06995,MA0125.1;0.986127,MA0130.1;0,MA0131.1;0.625452,MA0132.1;0,MA0133.1;0,MA0135.1;0.90122,MA0136.1;0.521435,MA0139.1;0.129876,MA0140.1;0.474342,MA0141.1;0.322254,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;0.1885,MA0145.1;0.706237,MA0146.1;0.319685,MA0147.1;0.607251,MA0148.1;0.439278,MA0149.1;0.464973,MA0062.2;0.135498,MA0035.2;0.473658,MA0039.2;0.679176,MA0138.2;0.608783,MA0002.2;1.45266,MA0137.2;0.28622,MA0104.2;0.486672,MA0047.2;0.542971,MA0112.2;1.48222,MA0065.2;1.10761,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;0.842081,MA0155.1;0.359913,MA0156.1;0.288314,MA0157.1;0.652111,MA0158.1;0,MA0159.1;1.14546,MA0160.1;0.453945,MA0161.1;0,MA0162.1;0.502732,MA0163.1;0.216998,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;3.10615,MA0079.2;0.379791,MA0102.2;1.41188,MA0258.1;0.180288,MA0259.1;0.218904,MA0442.1;0
}}
}}

Revision as of 19:31, 22 January 2013


Full id: C866_hairy_CD14_mycosis_cord_Eosinophils_CD14CD16_immature



Phase1 CAGE Peaks

Hg19::chr10:104155680..104155687,+p6@NFKB2
Hg19::chr11:117699420..117699434,-p4@FXYD2
Hg19::chr11:117699438..117699449,-p8@FXYD2
Hg19::chr11:117712764..117712789,-p@chr11:117712764..117712789
-
Hg19::chr20:61077113..61077116,+p@chr20:61077113..61077116
+
Hg19::chr22:24801933..24801943,+p@chr22:24801933..24801943
+
Hg19::chr2:114132562..114132577,-p@chr2:114132562..114132577
-
Hg19::chr6:160411448..160411452,+p@chr6:160411448..160411452
+
Hg19::chr7:45017046..45017066,-p6@MYO1G


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:0002266follicular dendritic cell activation0.00551908867851121
GO:0002268follicular dendritic cell differentiation0.00551908867851121
GO:0033257Bcl3/NF-kappaB2 complex0.00551908867851121
GO:0033256I-kappaB/NF-kappaB complex0.00551908867851121
GO:0048536spleen development0.00735835166545414
GO:0002467germinal center formation0.00735835166545414
GO:0043234protein complex0.010903573526755
GO:0005890sodium:potassium-exchanging ATPase complex0.0110362278570225
GO:0032991macromolecular complex0.0187566168636969
GO:0005391sodium:potassium-exchanging ATPase activity0.0187566168636969
GO:0030198extracellular matrix organization and biogenesis0.0460998883929867



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 monocyte2.06e-11142
CD14-positive, CD16-negative classical monocyte2.06e-11142
defensive cell2.98e-9648
phagocyte2.98e-9648
macrophage dendritic cell progenitor2.20e-7661
monopoietic cell5.01e-7559
monocyte5.01e-7559
monoblast5.01e-7559
promonocyte5.01e-7559
myeloid leukocyte1.84e-7072
granulocyte monocyte progenitor cell9.31e-6967
myeloid lineage restricted progenitor cell3.71e-6666
leukocyte8.73e-59136
myeloid cell1.07e-53108
common myeloid progenitor1.07e-53108
nongranular leukocyte2.78e-52115
hematopoietic lineage restricted progenitor cell1.03e-49120
stuff accumulating cell1.11e-4887
hematopoietic cell1.48e-48177
hematopoietic oligopotent progenitor cell8.41e-46161
hematopoietic multipotent progenitor cell8.41e-46161
hematopoietic stem cell2.05e-45168
angioblastic mesenchymal cell2.05e-45168
mesenchymal cell2.26e-15354
connective tissue cell7.62e-15361
motile cell5.52e-13386
intermediate monocyte7.52e-139
CD14-positive, CD16-positive monocyte7.52e-139
multi fate stem cell1.03e-10427
basophil1.77e-103
somatic stem cell2.12e-10433
Langerhans cell2.40e-105
stem cell5.38e-10441
circulating cell6.03e-096
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.37e-6098
blood island3.37e-6098
bone marrow1.51e-5976
hemolymphoid system3.11e-56108
immune system7.44e-5593
bone element1.62e-5482
skeletal element7.66e-4990
skeletal system5.15e-43100
lateral plate mesoderm1.37e-23203
musculoskeletal system6.58e-22167
connective tissue4.00e-14371
mesoderm1.96e-11315
mesoderm-derived structure1.96e-11315
presumptive mesoderm1.96e-11315


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)
MA0003.10.0416606
MA0004.11.06719
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.367355
MA0017.10.815464
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.11.28049
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.11.41801
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.11.02363
MA0056.10
MA0057.10.253359
MA0058.10.86817
MA0059.10.865474
MA0060.10.162248
MA0061.10.851955
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.354973
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.447621
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.12.03788
MA0084.11.37471
MA0087.10.838229
MA0088.10.650888
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.993944
MA0093.11.35827
MA0095.10
MA0098.10
MA0100.11.30927
MA0101.10.746654
MA0103.10.257174
MA0105.10.496814
MA0106.10.554855
MA0107.11.11943
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.582067
MA0115.11.11137
MA0116.11.13131
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.706237
MA0146.10.319685
MA0147.10.607251
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.679176
MA0138.20.608783
MA0002.21.45266
MA0137.20.28622
MA0104.20.486672
MA0047.20.542971
MA0112.21.48222
MA0065.21.10761
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.842081
MA0155.10.359913
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.11.14546
MA0160.10.453945
MA0161.10
MA0162.10.502732
MA0163.10.216998
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.23.10615
MA0079.20.379791
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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#10538410.82568968546830.0003028438388965950.00312444015514388
EBF1#187943.958429709586220.012557390254080.0454145467395895
FOSL1#8061313.23785990545770.001195916083435590.00811251492841836
JUNB#3726310.20354421994040.002524179606138380.013994945792084



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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