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Coexpression cluster:C1787: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;2.72292,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;2.48957,MA0017.1;1.24112,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;4.09095,MA0046.1;1.10134,MA0048.1;0.569896,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;3.05948,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.782425,MA0074.1;1.73427,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;3.01022,MA0103.1;0.442769,MA0105.1;1.58771,MA0106.1;0.779931,MA0107.1;3.60303,MA0108.2;0.94238,MA0109.1;0,MA0111.1;1.40074,MA0113.1;0.797251,MA0114.1;1.72991,MA0115.1;1.35895,MA0116.1;0.994489,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;1.39016,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.938075,MA0145.1;0.868598,MA0146.1;0.6031,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;0.858845,MA0047.2;0.767096,MA0112.2;0.839774,MA0065.2;1.41695,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.514087,MA0155.1;0.409315,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;1.00463,MA0160.1;0.669748,MA0161.1;0,MA0162.1;2.27598,MA0163.1;2.54221,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;4.41372,MA0099.2;0.699641,MA0079.2;0.340387,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:11, 22 January 2013


Full id: C1787_embryonic_Eosinophils_CD34_CD14_immature_Basophils_CD19



Phase1 CAGE Peaks

Hg19::chr17:4852857..4852892,+p@chr17:4852857..4852892
+
Hg19::chr17:73257101..73257120,+p@chr17:73257101..73257120
+
Hg19::chr5:176881716..176881752,+p3@PRR7
Hg19::chr5:176881798..176881811,+p5@PRR7
Hg19::chrX:153626083..153626119,+p6@RPL10


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:0005842cytosolic large ribosomal subunit (sensu Eukaryota)0.0360591075002943
GO:0005830cytosolic ribosome (sensu Eukaryota)0.0360591075002943
GO:0015934large ribosomal subunit0.0360591075002943
GO:0044445cytosolic part0.0461556576003768
GO:0033279ribosomal subunit0.0461556576003768



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
leukocyte8.96e-44136
nongranular leukocyte3.76e-35115
classical monocyte1.67e-3442
CD14-positive, CD16-negative classical monocyte1.67e-3442
hematopoietic lineage restricted progenitor cell2.86e-34120
hematopoietic stem cell6.85e-34168
angioblastic mesenchymal cell6.85e-34168
hematopoietic cell1.90e-33177
hematopoietic oligopotent progenitor cell3.11e-30161
hematopoietic multipotent progenitor cell3.11e-30161
myeloid leukocyte1.52e-2872
defensive cell6.70e-2848
phagocyte6.70e-2848
granulocyte monocyte progenitor cell2.10e-2467
macrophage dendritic cell progenitor6.56e-2461
monopoietic cell3.25e-2259
monocyte3.25e-2259
monoblast3.25e-2259
promonocyte3.25e-2259
myeloid lineage restricted progenitor cell4.15e-2266
myeloid cell2.20e-18108
common myeloid progenitor2.20e-18108
stuff accumulating cell1.53e-1387
lymphocyte3.46e-1153
common lymphoid progenitor3.46e-1153
lymphoid lineage restricted progenitor cell9.19e-1152
nucleate cell2.26e-1055
mesenchymal cell5.07e-08354
connective tissue cell2.77e-07361
motile cell8.89e-07386
granulocyte9.37e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.41e-2198
blood island1.41e-2198
bone marrow3.10e-2176
bone element2.68e-2082
hemolymphoid system3.44e-18108
immune system3.92e-1793
skeletal element9.29e-1790
skeletal system5.78e-14100
connective tissue8.17e-07371


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)
MA0003.12.72292
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.12.48957
MA0017.11.24112
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
MA0043.14.09095
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.13.05948
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.782425
MA0074.11.73427
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.13.01022
MA0103.10.442769
MA0105.11.58771
MA0106.10.779931
MA0107.13.60303
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.11.72991
MA0115.11.35895
MA0116.10.994489
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
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.868598
MA0146.10.6031
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
MA0104.20.858845
MA0047.20.767096
MA0112.20.839774
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.12.27598
MA0163.12.54221
MA0164.10.810347
MA0080.20.456437
MA0018.24.41372
MA0099.20.699641
MA0079.20.340387
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
BCL11A#53335211.34778204144280.01157056933741320.0422878881239536
CTCFL#140690311.84788461538460.001201770348538230.00815063922533828
ELF1#199743.406478367046030.01235066105299550.0447366104711197
ETS1#211335.83725655332140.009253279045631430.0349740594327845
GABPB1#255345.654147068945740.001776696502096670.0109086658425911
JUNB#3726212.24425306392850.009990490593345960.0374702595374007
MEF2A#4205311.24593854578640.001399366787411950.00910298772410566
NANOG#79923211.69791139240510.01091164951956080.0402259712027325
NFKB1#479055.488063424193840.0002008162847462320.00239090879646736
SMARCA4#6597262.70636132315520.0004014120859405330.00386637248395678
TAF1#687253.343046285745290.002394600090870310.0135344538851826
TCF12#693848.507571921749140.0003614215578492260.00361141466515646
TFAP2C#702236.485537165916130.006858951517940.0290605289079974
ZEB1#6935310.13305921052630.001895556924357070.0111620472272738
ZNF143#770238.100525931336740.003624870512090980.018332180108095



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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