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Coexpression cluster:C578: Difference between revisions

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{{Coexpression_clusters
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|full_id=C578_CD34_Natural_CD8_CD4_CD133_Basophils_CD14
|id=C578
}}

Latest revision as of 11:26, 17 September 2013


Full id: C578_CD34_Natural_CD8_CD4_CD133_Basophils_CD14



Phase1 CAGE Peaks

Hg19::chr10:12390958..12390973,-p@chr10:12390958..12390973
-
Hg19::chr12:76952682..76952690,-p@chr12:76952682..76952690
-
Hg19::chr13:101326316..101326335,+p@chr13:101326316..101326335
+
Hg19::chr14:105760706..105760717,-p@chr14:105760706..105760717
-
Hg19::chr14:105760904..105760918,+p@chr14:105760904..105760918
+
Hg19::chr15:52970999..52971015,+p@chr15:52970999..52971015
+
Hg19::chr15:52971052..52971073,+p@chr15:52971052..52971073
+
Hg19::chr19:33865006..33865017,-p@chr19:33865006..33865017
-
Hg19::chr1:221916028..221916038,+p@chr1:221916028..221916038
+
Hg19::chr2:122457110..122457118,-p@chr2:122457110..122457118
-
Hg19::chr2:28571261..28571277,+p@chr2:28571261..28571277
+
Hg19::chr6:16762361..16762374,-p@chr6:16762361..16762374
-
Hg19::chr6:34205792..34205795,-p@chr6:34205792..34205795
-
Hg19::chr7:141401439..141401452,+p@chr7:141401439..141401452
+
Hg19::chr8:145013517..145013546,+p@chr8:145013517..145013546
+


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
leukocyte2.90e-30136
hematopoietic stem cell4.50e-27168
angioblastic mesenchymal cell4.50e-27168
hematopoietic cell3.58e-25177
CD4-positive, alpha-beta T cell3.82e-216
hematopoietic oligopotent progenitor cell1.33e-19161
hematopoietic multipotent progenitor cell1.33e-19161
hematopoietic lineage restricted progenitor cell2.83e-19120
nongranular leukocyte6.71e-19115
mature alpha-beta T cell6.61e-1818
alpha-beta T cell6.61e-1818
immature T cell6.61e-1818
mature T cell6.61e-1818
immature alpha-beta T cell6.61e-1818
lymphoid lineage restricted progenitor cell1.40e-1552
lymphocyte3.32e-1553
common lymphoid progenitor3.32e-1553
nucleate cell1.70e-1455
T cell2.74e-1225
pro-T cell2.74e-1225
natural killer cell4.80e-123
pro-NK cell4.80e-123
basophil3.08e-113
naive T cell4.05e-113
plasmacytoid dendritic cell7.21e-113
single nucleate cell1.11e-103
mononuclear cell1.11e-103
myeloid leukocyte5.30e-0972
regulatory T cell9.03e-082
CD4-positive, CD25-positive, alpha-beta regulatory T cell9.03e-082
naive regulatory T cell9.03e-082
mesenchymal cell1.45e-07354
connective tissue cell3.12e-07361
myeloid cell3.78e-07108
common myeloid progenitor3.78e-07108
granulocyte4.35e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.32e-0998
blood island2.32e-0998
hemolymphoid system4.58e-08108
thymus8.56e-084
hemolymphoid system gland8.56e-084
thymic region8.56e-084
pharyngeal gland8.56e-084
thymus primordium8.56e-084
immune system5.97e-0793
connective tissue8.80e-07371


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)
MA0003.13.138
MA0004.10.256222
MA0006.10.842675
MA0007.10.241375
MA0009.10.669377
MA0014.11.50083
MA0017.10.16476
MA0019.11.75672
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.889224
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.23222
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.0510304
MA0056.10
MA0057.10.420982
MA0058.10.182945
MA0059.10.536577
MA0060.10.0671843
MA0061.11.64561
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.11.37852
MA0069.10.655419
MA0070.10.644843
MA0071.10.831024
MA0072.10.640598
MA0073.15.00938
MA0074.10.337035
MA0076.11.07748
MA0077.10.633326
MA0078.10.424186
MA0081.10.536866
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.426561
MA0089.10
MA0090.10.205547
MA0091.10.258318
MA0092.10.228476
MA0093.10.431889
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.12.00227
MA0103.10.411001
MA0105.12.1572
MA0106.10.37688
MA0107.11.08326
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.11.01449
MA0114.10.30732
MA0115.10.900969
MA0116.11.09759
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.181369
MA0140.10.30631
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.0838502
MA0145.11.3964
MA0146.11.62526
MA0147.11.11205
MA0148.10.276339
MA0149.10.298252
MA0062.20.425026
MA0035.20.305721
MA0039.20.122601
MA0138.20.425279
MA0002.20.82964
MA0137.20.153033
MA0104.21.31795
MA0047.20.366327
MA0112.20.258654
MA0065.20.491386
MA0150.11.10274
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.912675
MA0155.12.06149
MA0156.10.91467
MA0157.11.17385
MA0158.10
MA0159.11.11468
MA0160.10.288813
MA0161.10
MA0162.10.76493
MA0163.12.60708
MA0164.10.402162
MA0080.20.432036
MA0018.20.378086
MA0099.20.312108
MA0079.24.49499
MA0102.21.1957
MA0258.10.27007
MA0259.10.104286
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
CTCF#1066482.858803398973350.002681647271099090.0147723276199334
E2F1#186982.617274247935640.004786085608563210.0224906184419678
EBF1#187984.750115651503477.80369455890836e-050.00120225705271844
POLR2A#5430121.717962541246460.008857472838871370.0336167456144664
TFAP2C#702253.603076203286740.009206120583810160.0348071544601437



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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