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Coexpression cluster:C4589: Difference between revisions

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{{Coexpression_clusters
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,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,6.03433,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,1.94915,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,1.95727,0.845342,1.53533,1.7611,2.30584,1.05396,0.842925,0.645155,1.00813,0.795576,1.21459,0.534793,1.11965,0.599922,1.36391,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,1.54087,1.44641,0.726632,0.939121,0.808003,1.28131,0.645308,1.02504,0.951993,1.60305,1.29475,1.45259,0.928548,0.650353,0.892517,2.67708,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,3.20161,0.333216,1.45054,0.430728,0.414196,1.02656,1.12884,1.20029,1.74644,0.459024,1.14559,0.960908,1.24629,1.39759,0.169933,0.303648,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,4.5214,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,2.55998,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,2.3166,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,2.29164,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.42224|tfbs_overrepresentation_jaspar=MA0003.1;0.401049,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;2.4146,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;2.99448,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;1.04561,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;13.9778,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;1.70054,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;1.31954,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;3.60951,MA0101.1;1.55947,MA0103.1;0.628063,MA0105.1;9.84291,MA0106.1;0.986396,MA0107.1;2.34614,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;1.96087,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.752137,MA0146.1;0.707589,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.62945,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;2.97249,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.838867,MA0155.1;2.83144,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;1.38935,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.776149,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;11.5899,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4589_Neutrophils_Eosinophils_acute_CD8_Whole_thymus_CD4
|id=C4589
}}

Latest revision as of 14:15, 17 September 2013


Full id: C4589_Neutrophils_Eosinophils_acute_CD8_Whole_thymus_CD4



Phase1 CAGE Peaks

Hg19::chr6:30652445..30652456,-p14@PPP1R18
Hg19::chr6:30652466..30652492,-p8@PPP1R18
Hg19::chr6:30652497..30652508,-p13@PPP1R18


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
hematopoietic stem cell8.38e-55168
angioblastic mesenchymal cell8.38e-55168
hematopoietic cell4.35e-53177
hematopoietic oligopotent progenitor cell2.46e-51161
hematopoietic multipotent progenitor cell2.46e-51161
leukocyte1.50e-45136
nongranular leukocyte8.53e-39115
hematopoietic lineage restricted progenitor cell4.93e-37120
myeloid cell9.83e-32108
common myeloid progenitor9.83e-32108
myeloid leukocyte5.95e-2672
granulocyte monocyte progenitor cell1.41e-2067
myeloid lineage restricted progenitor cell4.10e-2066
multi fate stem cell1.02e-19427
monopoietic cell1.26e-1959
monocyte1.26e-1959
monoblast1.26e-1959
promonocyte1.26e-1959
mesenchymal cell4.35e-19354
somatic stem cell1.02e-18433
macrophage dendritic cell progenitor1.16e-1861
connective tissue cell3.81e-18361
stem cell4.69e-18441
defensive cell1.95e-1748
phagocyte1.95e-1748
lymphoid lineage restricted progenitor cell2.83e-1752
lymphocyte3.65e-1753
common lymphoid progenitor3.65e-1753
nucleate cell2.98e-1655
classical monocyte3.04e-1542
CD14-positive, CD16-negative classical monocyte3.04e-1542
motile cell7.20e-13386
endothelial cell6.22e-1236
T cell1.09e-1025
pro-T cell1.09e-1025
endothelial cell of vascular tree2.13e-1024
mature alpha-beta T cell9.77e-1018
alpha-beta T cell9.77e-1018
immature T cell9.77e-1018
mature T cell9.77e-1018
immature alpha-beta T cell9.77e-1018
somatic cell1.09e-08588
blood vessel endothelial cell1.41e-0818
embryonic blood vessel endothelial progenitor cell1.41e-0818
CD8-positive, alpha-beta T cell4.32e-0811
meso-epithelial cell9.33e-0845
Uber Anatomy
Ontology termp-valuen
hemolymphoid system5.95e-28108
lateral plate mesoderm2.17e-26203
hematopoietic system3.74e-2698
blood island3.74e-2698
immune system6.48e-2293
bone marrow2.24e-1776
connective tissue1.07e-16371
bone element7.23e-1582
skeletal element6.30e-1290
cardiovascular system1.76e-11109
mesoderm1.83e-11315
mesoderm-derived structure1.83e-11315
presumptive mesoderm1.83e-11315
circulatory system6.73e-11112
vessel1.37e-1068
skeletal system2.95e-10100
epithelial tube open at both ends3.60e-1059
blood vessel3.60e-1059
blood vasculature3.60e-1059
vascular cord3.60e-1059
vasculature6.12e-0978
vascular system6.12e-0978
blood vessel endothelium1.41e-0818
endothelium1.41e-0818
cardiovascular system endothelium1.41e-0818
musculoskeletal system3.59e-08167
splanchnic layer of lateral plate mesoderm2.57e-0783
blood3.73e-0715
haemolymphatic fluid3.73e-0715
organism substance3.73e-0715
artery5.30e-0742
arterial blood vessel5.30e-0742
arterial system5.30e-0742
Disease
Ontology termp-valuen
leukemia6.25e-0939
hematologic cancer6.59e-0951
immune system cancer6.59e-0951
myeloid leukemia7.24e-0831


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.12.4146
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.12.99448
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.113.9778
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.13.60951
MA0101.11.55947
MA0103.10.628063
MA0105.19.84291
MA0106.10.986396
MA0107.12.34614
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.22.97249
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.12.83144
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.211.5899
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
EGR1#195834.988179094810140.008056488137383440.0322219417370731
ELF1#199734.258097958807540.01295179875054610.0464644445489243
NFKB1#479035.488063424193840.006049381815655430.0270701995563322
ZBTB7A#5134137.35190930787590.002516255860282270.0140818371981577



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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