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Coexpression cluster:C1148: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;1.04589,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.0723474,MA0017.1;1.75854,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,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;0.382278,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;1.01052,MA0056.1;0,MA0057.1;0.369442,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;4.49289,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;1.04478,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.538456,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;0.621149,MA0101.1;0.918548,MA0103.1;0.332048,MA0105.1;0.340955,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;2.09327,MA0115.1;2.7254,MA0116.1;0.277571,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;0.614215,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;1.04059,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.708913,MA0145.1;0.581146,MA0146.1;1.54462,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;1.07166,MA0035.2;0.564239,MA0039.2;2.64992,MA0138.2;0.704862,MA0002.2;1.15032,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.0758925,MA0065.2;0.591589,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;0.534073,MA0156.1;0.959643,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.770207,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.485816,MA0163.1;0.632664,MA0164.1;1.62495,MA0080.2;1.63199,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;4.01,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:44, 22 January 2013


Full id: C1148_CD14_Eosinophils_Mast_Neutrophils_CD14CD16_blood_Basophils



Phase1 CAGE Peaks

Hg19::chr11:65186701..65186725,+p@chr11:65186701..65186725
+
Hg19::chr18:3448314..3448333,+p18@TGIF1
Hg19::chr19:12897222..12897231,+p@chr19:12897222..12897231
+
Hg19::chr2:157190968..157190980,-p@chr2:157190968..157190980
-
Hg19::chr2:28614676..28614691,+p@chr2:28614676..28614691
+
Hg19::chr2:28614747..28614759,+p@chr2:28614747..28614759
+
Hg19::chr8:17940787..17940819,-p@chr8:17940787..17940819
-


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
myeloid leukocyte6.32e-3872
classical monocyte5.79e-3642
CD14-positive, CD16-negative classical monocyte5.79e-3642
leukocyte5.04e-35136
defensive cell1.01e-3448
phagocyte1.01e-3448
granulocyte monocyte progenitor cell1.84e-3367
macrophage dendritic cell progenitor1.61e-3261
myeloid lineage restricted progenitor cell2.21e-3266
monopoietic cell4.98e-3159
monocyte4.98e-3159
monoblast4.98e-3159
promonocyte4.98e-3159
hematopoietic lineage restricted progenitor cell2.06e-29120
nongranular leukocyte3.33e-27115
hematopoietic stem cell2.43e-25168
angioblastic mesenchymal cell2.43e-25168
hematopoietic cell6.84e-25177
myeloid cell4.39e-24108
common myeloid progenitor4.39e-24108
hematopoietic oligopotent progenitor cell1.09e-23161
hematopoietic multipotent progenitor cell1.09e-23161
stuff accumulating cell2.61e-1387
intermediate monocyte9.38e-099
CD14-positive, CD16-positive monocyte9.38e-099
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.47e-3698
blood island1.47e-3698
hemolymphoid system1.56e-33108
bone marrow7.22e-3176
bone element2.66e-2882
immune system1.02e-2793
skeletal element3.53e-2690
skeletal system1.14e-21100
lateral plate mesoderm1.76e-18203
musculoskeletal system1.49e-10167
mesoderm1.37e-08315
mesoderm-derived structure1.37e-08315
presumptive mesoderm1.37e-08315


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)
MA0003.11.04589
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0723474
MA0017.11.75854
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
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
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.11.01052
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.14.49289
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.12.09327
MA0115.12.7254
MA0116.10.277571
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
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.11.04059
MA0142.10.777365
MA0143.10.66587
MA0144.10.708913
MA0145.10.581146
MA0146.11.54462
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.21.07166
MA0035.20.564239
MA0039.22.64992
MA0138.20.704862
MA0002.21.15032
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.591589
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.534073
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.770207
MA0160.10.543522
MA0161.10
MA0162.10.485816
MA0163.10.632664
MA0164.11.62495
MA0080.21.63199
MA0018.20.650405
MA0099.20.572
MA0079.24.01
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
E2F1#186953.505278010628090.005090553587915050.0236858382860313
E2F6#187653.583682665498130.004598101897827240.0217245493828174
HEY1#2346252.885793602218360.01231366941853030.0446227383900723
HMGN3#932444.673455841914620.005751881099938870.0259065339915696
HNF4A#3172413.21845163597350.0001099302546513230.00152835541340914
HNF4G#3174312.32289536847720.001324450221997230.00879198224974062
MEF2C#4208211.80324414074970.01134538181234960.0415973435527464
NR3C1#2908510.69501666512362.48694675006425e-050.000538532514264898
NR4A1#31641394.0874200426440.002534791264696470.0140358976137869
SIN3A#2594253.863489090582240.003248465677640770.0168286957791232
SMARCC2#6601226.90153555054220.002285195715908250.0129708454007468
STAT3#677446.011122855516710.002255779156394480.0128108384619186



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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