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Coexpression cluster:C1224: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.00215847,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.0156227,MA0017.1;0.380797,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;1.29551,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.120314,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.0407081,MA0056.1;0,MA0057.1;0.115382,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;0.575931,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;2.88764,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;1.70839,MA0074.1;0.60198,MA0076.1;0.422297,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;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.104569,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;0.269076,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;2.36239,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;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;2.02038,MA0145.1;0.0807715,MA0146.1;0.0127148,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.00276064,MA0138.2;0.704862,MA0002.2;5.15968,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.0758925,MA0065.2;0.282161,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.335384,MA0155.1;0.071478,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.25944,MA0163.1;0.382702,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;9.15802e-07,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:47, 22 January 2013


Full id: C1224_CD4_xeroderma_splenic_CD8_Peripheral_Natural_lymph



Phase1 CAGE Peaks

Hg19::chr16:84801852..84801877,+p@chr16:84801852..84801877
+
Hg19::chr2:242051921..242051933,-p15@PASK
Hg19::chr2:242051966..242051973,-p14@PASK
Hg19::chr2:242051975..242051994,-p2@PASK
Hg19::chr2:242051995..242052016,-p7@PASK
Hg19::chr2:242052022..242052034,-p11@PASK
Hg19::chr2:242052089..242052103,-p9@PASK


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
mature alpha-beta T cell8.23e-4818
alpha-beta T cell8.23e-4818
immature T cell8.23e-4818
mature T cell8.23e-4818
immature alpha-beta T cell8.23e-4818
lymphoid lineage restricted progenitor cell1.19e-3752
T cell3.78e-3725
pro-T cell3.78e-3725
lymphocyte8.49e-3753
common lymphoid progenitor8.49e-3753
nucleate cell3.49e-3555
CD8-positive, alpha-beta T cell6.74e-3311
nongranular leukocyte3.98e-21115
leukocyte2.19e-20136
CD4-positive, alpha-beta T cell1.48e-196
hematopoietic lineage restricted progenitor cell1.33e-15120
hematopoietic stem cell8.90e-15168
angioblastic mesenchymal cell8.90e-15168
hematopoietic cell1.42e-13177
hematopoietic oligopotent progenitor cell1.90e-12161
hematopoietic multipotent progenitor cell1.90e-12161
single nucleate cell1.52e-103
mononuclear cell1.52e-103
naive T cell2.45e-103
natural killer cell3.91e-103
pro-NK cell3.91e-103
regulatory T cell3.52e-072
CD4-positive, CD25-positive, alpha-beta regulatory T cell3.52e-072
naive regulatory T cell3.52e-072
Uber Anatomy
Ontology termp-valuen
hemopoietic organ4.51e-157
immune organ4.51e-157
spleen8.42e-103
gastrointestinal system mesentery8.42e-103
stomach region8.42e-103
mesentery8.42e-103
gastrointestinal system serosa8.42e-103
mesentery of stomach8.42e-103
gut mesentery8.42e-103
dorsal mesentery8.42e-103
dorsal mesogastrium8.42e-103
peritoneal cavity8.42e-103
spleen primordium8.42e-103
thymus2.66e-074
hemolymphoid system gland2.66e-074
thymic region2.66e-074
pharyngeal gland2.66e-074
thymus primordium2.66e-074
blood5.77e-0715
haemolymphatic fluid5.77e-0715
organism substance5.77e-0715


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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.380797
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
MA0041.11.29551
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.12.88764
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.11.70839
MA0074.10.60198
MA0076.10.422297
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
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.12.36239
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
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.12.02038
MA0145.10.0807715
MA0146.10.0127148
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.00276064
MA0138.20.704862
MA0002.25.15968
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.25944
MA0163.10.382702
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.29.15802e-07
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
BCL11A#53335624.31667580309181.29931738009616e-089.60363820664283e-07
EBF1#187967.634114439916291.2666377582912e-050.000312143418683752
MEF2A#4205616.06562649398061.53846883349817e-078.6292237648612e-06
MEF2C#4208635.40973242224921.3745684456669e-091.23438137486677e-07
NFKB1#479064.704054363594720.000216115061401970.00247786155426066
SP1#666764.884326895549340.0001736361122290910.00211331801947255



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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