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Coexpression cluster:C1776: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,0.454983,0.653236,0.733342,0.866061,0.321368,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,1.42981,0.501863,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.758594,1.0713,1.1597,0.413782,0.654459,1.78381,0.301779,1.06799,0.580638,0.132849,0.451846,0.476793,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,1.58259,0.554326,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,1.34093,0.796279,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,0.647361,0.844289,1.79645,3.13513,1.15413,1.01895,0.367039,0.455791,0.381528,0.780629,1.06255,0.849074,1.14173,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,1.18046,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,1.65153,1.73625,0.0214572
|tfbs_overrepresentation_jaspar=MA0003.1;0.00991994,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.0418333,MA0017.1;0.496101,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;0.288856,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;1.29682,MA0060.1;0.321781,MA0061.1;1.44118,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;0.00220137,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;1.2972,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,MA0089.1;0,MA0090.1;1.36977,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;1.00065,MA0106.1;0.779931,MA0107.1;0.985964,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,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;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.442008,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.15493,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;0.880827,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.514087,MA0155.1;0.130813,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;1.00463,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.0592265,MA0163.1;0.168633,MA0164.1;3.15573,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.000396307,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;1.02361,MA0442.1;0
}}
}}

Revision as of 20:10, 22 January 2013


Full id: C1776_embryonic_CD8_Natural_Whole_NK_blood_Basophils



Phase1 CAGE Peaks

Hg19::chr17:34199262..34199274,-p@chr17:34199262..34199274
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Hg19::chr17:34199297..34199315,-p@chr17:34199297..34199315
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Hg19::chr17:34205568..34205579,-p@chr17:34205568..34205579
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Hg19::chr17:34205625..34205636,-p@chr17:34205625..34205636
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Hg19::chr17:34207354..34207372,-p1@CCL5


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
nongranular leukocyte1.02e-29115
leukocyte4.32e-29136
hematopoietic cell4.83e-28177
hematopoietic stem cell1.13e-27168
angioblastic mesenchymal cell1.13e-27168
hematopoietic oligopotent progenitor cell1.41e-26161
hematopoietic multipotent progenitor cell1.41e-26161
hematopoietic lineage restricted progenitor cell7.10e-25120
mature alpha-beta T cell1.22e-1718
alpha-beta T cell1.22e-1718
immature T cell1.22e-1718
mature T cell1.22e-1718
immature alpha-beta T cell1.22e-1718
defensive cell5.39e-1648
phagocyte5.39e-1648
CD8-positive, alpha-beta T cell6.43e-1611
classical monocyte2.49e-1542
CD14-positive, CD16-negative classical monocyte2.49e-1542
myeloid leukocyte3.31e-1572
macrophage dendritic cell progenitor5.53e-1561
monopoietic cell7.54e-1559
monocyte7.54e-1559
monoblast7.54e-1559
promonocyte7.54e-1559
myeloid cell3.66e-14108
common myeloid progenitor3.66e-14108
lymphoid lineage restricted progenitor cell8.47e-1352
T cell9.17e-1325
pro-T cell9.17e-1325
granulocyte monocyte progenitor cell1.02e-1267
lymphocyte2.18e-1253
common lymphoid progenitor2.18e-1253
myeloid lineage restricted progenitor cell3.28e-1266
nucleate cell1.29e-1155
circulating cell3.97e-086
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.18e-2498
blood island1.18e-2498
hemolymphoid system6.60e-24108
blood2.78e-1915
haemolymphatic fluid2.78e-1915
organism substance2.78e-1915
immune system1.79e-1293
bone marrow9.73e-1176
larynx7.13e-109
bone element3.06e-0982
lateral plate mesoderm1.02e-08203
upper respiratory tract9.86e-0819
skeletal element1.35e-0790
skeletal system5.78e-07100


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)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
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
MA0055.10.288856
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.11.29682
MA0060.10.321781
MA0061.11.44118
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.11.36977
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.11.00065
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
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
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.168633
MA0164.13.15573
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.000396307
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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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