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Coexpression cluster:C1988: Difference between revisions

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{{Coexpression_clusters
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.0854747,0.0747609,0.406458,0.312881,0.512825,0.244656,0.192188,0.158985,0.174153,0.0972854,0.333309,0.249919,0.339517,0.303699,0.198326,0.394084,0.458518,0.282501,0.252005,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.117618,0.014271,0.396962,0.316002,0.0618069,0.321404,0.225079,0.300542,0.379651,0.185715,0.0680703,0.375521,0.271405,0.311201,0.221943,0.306427,0.367733,0.246925,0.0234915,0.390438,0.343014,0.270094,0.276922,0.156279,0.313647,0.461742,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.0735747,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.508546,0.224871,0.398887,0.389061,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.0642384,0.344469,0.184651,0.0515336,0.297596,0.42392,0.425912,0.380826,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,0.13907,0.470121,0.269432,0.250466,0.409882,0.115686,0.0981568,0.162633,0.342661,0.27567,0.248127,0.33299,0.384731,0.319112,0.526476|tfbs_overrepresentation_for_novel_motifs=1.26722,0.0561813,0.500341,0.654974,0.454983,0.653236,0.733342,0.866061,0.859849,0.345702,1.50573,0.778743,0.274093,0.721271,1.14971,0.478935,0.963929,0.395009,0.287891,0.167776,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,1.45697,1.00172,1.68319,0.758594,0.417272,0.432883,0.413782,0.654459,0.388123,0.301779,1.06799,0.580638,0.821929,0.451846,0.218848,1.32072,0.734485,0.609718,3.22632,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,3.71681,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.709554,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,1.71087,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,1.11542,0.512457,1.05402,2.14231,0.631235,1.37132,1.05995,0.597842,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,2.32431,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.720819|tfbs_overrepresentation_jaspar=MA0003.1;0.481059,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;1.9468,MA0017.1;2.14806,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;1.05691,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.791444,MA0063.1;0,MA0066.1;5.61971,MA0067.1;1.43651,MA0068.1;1.28241,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;1.65981,MA0072.1;1.0812,MA0073.1;6.69924,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;3.23747,MA0081.1;1.2972,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;1.92154,MA0089.1;0,MA0090.1;2.34702,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;1.16366,MA0103.1;0.442769,MA0105.1;1.58771,MA0106.1;0.779931,MA0107.1;0.985964,MA0108.2;0.94238,MA0109.1;0,MA0111.1;2.39477,MA0113.1;0.797251,MA0114.1;3.56849,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;1.29278,MA0142.1;0.912455,MA0143.1;4.48146,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;0.333008,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.311551,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;7.03003,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;3.30401,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.0592265,MA0163.1;7.5271,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.146371,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0}}
|full_id=C1988_Macrophage_CD14_Hepatocyte_Monocytederived_liver_migratory_CD14CD16
|id=C1988
}}

Latest revision as of 11:56, 17 September 2013


Full id: C1988_Macrophage_CD14_Hepatocyte_Monocytederived_liver_migratory_CD14CD16



Phase1 CAGE Peaks

Hg19::chr7:150498348..150498411,-p2@TMEM176B
Hg19::chr7:150498413..150498425,-p6@TMEM176B
Hg19::chr7:150498426..150498465,-p3@TMEM176B
Hg19::chr7:150498588..150498601,+p6@TMEM176A
Hg19::chr7:150498610..150498659,+p4@TMEM176A


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><br>

Cell Type
Ontology termp-valuen
defensive cell8.24e-5448
phagocyte8.24e-5448
monopoietic cell4.08e-5059
monocyte4.08e-5059
monoblast4.08e-5059
promonocyte4.08e-5059
macrophage dendritic cell progenitor7.82e-4861
classical monocyte1.44e-4642
CD14-positive, CD16-negative classical monocyte1.44e-4642
myeloid lineage restricted progenitor cell9.77e-4366
granulocyte monocyte progenitor cell8.25e-4267
myeloid leukocyte1.51e-4072
myeloid cell2.46e-25108
common myeloid progenitor2.46e-25108
stuff accumulating cell1.09e-2487
nongranular leukocyte3.42e-22115
leukocyte3.33e-21136
hematopoietic lineage restricted progenitor cell1.24e-17120
hematopoietic stem cell5.66e-14168
angioblastic mesenchymal cell5.66e-14168
hematopoietic oligopotent progenitor cell1.18e-12161
hematopoietic multipotent progenitor cell1.18e-12161
hematopoietic cell2.63e-12177
macrophage1.89e-086
intermediate monocyte2.59e-089
CD14-positive, CD16-positive monocyte2.59e-089
Uber Anatomy
Ontology termp-valuen
bone marrow1.38e-3476
hematopoietic system3.85e-3498
blood island3.85e-3498
immune system6.03e-3393
hemolymphoid system1.12e-31108
bone element1.12e-3082
adult organism4.10e-27114
skeletal element2.66e-2690
skeletal system7.25e-22100
lateral plate mesoderm1.32e-13203
organ5.15e-13503
musculoskeletal system1.96e-11167
embryonic structure1.31e-10564
germ layer1.64e-10560
germ layer / neural crest1.64e-10560
embryonic tissue1.64e-10560
presumptive structure1.64e-10560
germ layer / neural crest derived structure1.64e-10560
epiblast (generic)1.64e-10560
developing anatomical structure4.02e-10581
embryo5.00e-10592
mesoderm2.98e-09315
mesoderm-derived structure2.98e-09315
presumptive mesoderm2.98e-09315
multi-cellular organism8.11e-09656
anatomical system2.43e-08624
anatomical group2.90e-08625


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)
MA0003.10.481059
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.9468
MA0017.12.14806
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.11.05691
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.791444
MA0063.10
MA0066.15.61971
MA0067.11.43651
MA0068.11.28241
MA0069.11.09737
MA0070.11.08584
MA0071.11.65981
MA0072.11.0812
MA0073.16.69924
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.13.23747
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.92154
MA0089.10
MA0090.12.34702
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.11.58771
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.12.39477
MA0113.10.797251
MA0114.13.56849
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.11.29278
MA0142.10.912455
MA0143.14.48146
MA0144.10.356507
MA0145.10.143698
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.311551
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.27.03003
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.13.30401
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.17.5271
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.146371
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
SUZ12#23512550.11578091106293.15480790456198e-092.62956889660454e-07



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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