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Coexpression cluster:C1216: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.465735,0.384703,0.529489,0.343148,0.52784,0.604235,0.643217,0.224331,0.443077,0.497563,0.647852,0.184039,1.44576,0.341795,0.365029,0.827563,1.43406,0.19568,0.66776,0.384762,1.29497,0.520063,0.338096,0.430372,1.60904,0.49486,0.517892,0.346214,0.898182,0.475674,0.864517,0.257226,0.186138,0.309012,0.71891,2.27897,0.529001,0.282922,0.207499,0.829015,0.459366,0.254304,0.340293,0.265117,1.06715,0.60533,0.486696,0.237549,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,1.44118,0.561701,0.905643,0.60771,0.224801,0.799729,1.51519,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.656075,3.10696,1.0929,0.179863,0.503161,0.921933,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.310394,5.13835,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,2.4654,0.277058,0.566252,0.924148,0.715799,1.32948,0.28424,0.875714,0.918549,0.831244,0.753567,1.23455,0.815341,0.589207,0.43012,0.873303,0.395884,0.915771,0.988112,0.507004,1.22894,0.304323,0.358137,0.474472,0.762789,0.736663,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.76179,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,1.18454,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,1.15519,0.722945,0.703388,3.06512,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.377843
|tfbs_overrepresentation_jaspar=MA0003.1;0.0462779,MA0004.1;0.502801,MA0006.1;0.904424,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.367415,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.940207,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.120314,MA0050.1;0.490116,MA0051.1;1.46692,MA0052.1;0.896548,MA0055.1;1.4376,MA0056.1;0,MA0057.1;0.369442,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;4.07054,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.488375,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.672652,MA0074.1;0.60198,MA0076.1;1.08222,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.0723293,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;1.50553,MA0101.1;1.64331,MA0103.1;0.332048,MA0105.1;1.14871,MA0106.1;0.648997,MA0107.1;2.1191,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.760835,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;1.491,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.980834,MA0146.1;0.324987,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;1.07166,MA0035.2;0.564239,MA0039.2;0.0170091,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.556641,MA0065.2;0.0828768,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.335384,MA0155.1;1.36741,MA0156.1;0.959643,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.770207,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.106355,MA0163.1;0.0167306,MA0164.1;0.678332,MA0080.2;0.911393,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.0232399,MA0102.2;1.51913,MA0258.1;0.687127,MA0259.1;0.787775,MA0442.1;0
}}
}}

Revision as of 19:46, 22 January 2013


Full id: C1216_immature_CD14_Natural_Peripheral_Mast_CD34_Basophils



Phase1 CAGE Peaks

Hg19::chr16:11945524..11945538,+p@chr16:11945524..11945538
+
Hg19::chr18:12991627..12991636,-p@chr18:12991627..12991636
-
Hg19::chr19:10514633..10514647,+p@chr19:10514633..10514647
+
Hg19::chr19:10514802..10514824,+p@chr19:10514802..10514824
+
Hg19::chr19:10519743..10519746,+p@chr19:10519743..10519746
+
Hg19::chr1:20987540..20987548,+p@chr1:20987540..20987548
+
Hg19::chr8:81399734..81399738,-p@chr8:81399734..81399738
-


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
leukocyte1.24e-58136
hematopoietic lineage restricted progenitor cell4.02e-49120
hematopoietic cell2.67e-48177
hematopoietic stem cell2.36e-47168
angioblastic mesenchymal cell2.36e-47168
nongranular leukocyte4.54e-46115
classical monocyte8.50e-4442
CD14-positive, CD16-negative classical monocyte8.50e-4442
hematopoietic oligopotent progenitor cell1.47e-41161
hematopoietic multipotent progenitor cell1.47e-41161
granulocyte monocyte progenitor cell2.80e-4067
myeloid leukocyte1.59e-3972
defensive cell1.76e-3748
phagocyte1.76e-3748
macrophage dendritic cell progenitor1.17e-3561
myeloid lineage restricted progenitor cell4.56e-3566
monopoietic cell3.41e-3159
monocyte3.41e-3159
monoblast3.41e-3159
promonocyte3.41e-3159
myeloid cell1.93e-29108
common myeloid progenitor1.93e-29108
intermediate monocyte2.27e-299
CD14-positive, CD16-positive monocyte2.27e-299
stuff accumulating cell9.66e-1887
mesenchymal cell3.20e-17354
connective tissue cell1.18e-16361
motile cell1.19e-14386
circulating cell2.36e-136
stem cell3.15e-12441
multi fate stem cell3.35e-12427
natural killer cell6.62e-123
pro-NK cell6.62e-123
somatic stem cell7.28e-12433
basophil3.78e-113
lymphoid lineage restricted progenitor cell3.81e-1152
lymphocyte7.20e-1153
common lymphoid progenitor7.20e-1153
single nucleate cell1.46e-103
mononuclear cell1.46e-103
nucleate cell2.39e-1055
non-classical monocyte5.37e-103
CD14-low, CD16-positive monocyte5.37e-103
T cell4.27e-0925
pro-T cell4.27e-0925
CD1a-positive Langerhans cell1.75e-082
immature CD1a-positive Langerhans cell1.75e-082
histamine secreting cell5.09e-075
biogenic amine secreting cell5.09e-075
granulocytopoietic cell5.09e-075
mast cell5.09e-075
mast cell progenitor5.09e-075
basophil mast progenitor cell5.09e-075
Langerhans cell7.60e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.46e-3798
blood island1.46e-3798
bone marrow3.98e-3776
bone element7.81e-3482
hemolymphoid system3.00e-33108
skeletal element4.02e-3090
immune system6.80e-2993
skeletal system2.58e-26100
connective tissue7.06e-16371
lateral plate mesoderm1.77e-13203
musculoskeletal system1.33e-12167


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)
MA0003.10.0462779
MA0004.10.502801
MA0006.10.904424
MA0007.10.483857
MA0009.10.973289
MA0014.10.367415
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.940207
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.11.46692
MA0052.10.896548
MA0055.11.4376
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.14.07054
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.672652
MA0074.10.60198
MA0076.11.08222
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.11.50553
MA0101.11.64331
MA0103.10.332048
MA0105.11.14871
MA0106.10.648997
MA0107.12.1191
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.760835
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.11.491
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.980834
MA0146.10.324987
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.21.07166
MA0035.20.564239
MA0039.20.0170091
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.556641
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.11.36741
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.770207
MA0160.10.543522
MA0161.10
MA0162.10.106355
MA0163.10.0167306
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.20.0232399
MA0102.21.51913
MA0258.10.687127
MA0259.10.787775
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
ELF1#199753.041498542005380.009719562269370750.0365657348024499
PAX5#507943.811180303530190.01208261681555190.0438295445659902
POU2F2#545245.203499461567160.003866714310179810.0190668449405509



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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