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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:48, 17 September 2013


Full id: C1590_Mast_CD19_Basophils_CD4_Natural_Eosinophils_CD8



Phase1 CAGE Peaks

Hg19::chr10:63806474..63806496,+p@chr10:63806474..63806496
+
Hg19::chr11:73694239..73694253,-p2@UCP2
Hg19::chr11:73694257..73694289,-p3@UCP2
Hg19::chr12:25539261..25539297,+p@chr12:25539261..25539297
+
Hg19::chr22:32188667..32188693,+p2@DEPDC5


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

GO IDGO nameFDR corrected p-value
GO:0000303response to superoxide0.00735856827869091
GO:0000305response to oxygen radical0.00735856827869091
GO:0000302response to reactive oxygen species0.0264822674140548
GO:0006839mitochondrial transport0.0352987719354742
GO:0007005mitochondrion organization and biogenesis0.0495752912277362
GO:0006979response to oxidative stress0.0495752912277362
GO:0015992proton transport0.0495752912277362
GO:0006818hydrogen transport0.0495752912277362



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
leukocyte1.35e-71136
hematopoietic stem cell8.81e-67168
angioblastic mesenchymal cell8.81e-67168
hematopoietic cell1.94e-63177
hematopoietic oligopotent progenitor cell3.71e-62161
hematopoietic multipotent progenitor cell3.71e-62161
hematopoietic lineage restricted progenitor cell9.24e-62120
nongranular leukocyte5.18e-57115
nucleate cell3.91e-3355
myeloid leukocyte1.13e-3172
lymphocyte1.15e-3153
common lymphoid progenitor1.15e-3153
lymphoid lineage restricted progenitor cell9.00e-3152
myeloid cell4.84e-29108
common myeloid progenitor4.84e-29108
granulocyte monocyte progenitor cell1.76e-2867
myeloid lineage restricted progenitor cell9.69e-2866
classical monocyte4.32e-2642
CD14-positive, CD16-negative classical monocyte4.32e-2642
macrophage dendritic cell progenitor3.98e-2361
monopoietic cell7.99e-2259
monocyte7.99e-2259
monoblast7.99e-2259
promonocyte7.99e-2259
defensive cell4.94e-2148
phagocyte4.94e-2148
lymphocyte of B lineage1.66e-1824
pro-B cell1.66e-1824
B cell3.06e-1514
mature alpha-beta T cell1.54e-1418
alpha-beta T cell1.54e-1418
immature T cell1.54e-1418
mature T cell1.54e-1418
immature alpha-beta T cell1.54e-1418
mesenchymal cell5.81e-13354
connective tissue cell1.82e-12361
T cell5.75e-1125
pro-T cell5.75e-1125
motile cell7.99e-10386
CD8-positive, alpha-beta T cell9.23e-1011
intermediate monocyte8.41e-089
CD14-positive, CD16-positive monocyte8.41e-089
CD4-positive, alpha-beta T cell1.06e-076
stuff accumulating cell4.01e-0787
histamine secreting cell8.74e-075
biogenic amine secreting cell8.74e-075
granulocytopoietic cell8.74e-075
mast cell8.74e-075
mast cell progenitor8.74e-075
basophil mast progenitor cell8.74e-075
granulocyte9.14e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.35e-3898
blood island9.35e-3898
hemolymphoid system2.83e-34108
immune system2.14e-2593
bone marrow6.48e-2576
bone element1.08e-2182
skeletal element4.01e-1890
skeletal system1.51e-14100
connective tissue3.38e-11371
blood2.22e-1015
haemolymphatic fluid2.22e-1015
organism substance2.22e-1015
lateral plate mesoderm4.12e-10203


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)
MA0003.10.136928
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
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
MA0041.11.55893
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.11.5062
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.12.35759
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.11.12656
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
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
MA0145.11.39943
MA0146.10.6031
MA0147.11.77656
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.21.54865
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.11.20729
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.0439995
MA0164.10.810347
MA0080.21.15604
MA0018.20.781393
MA0099.20.699641
MA0079.20.0198381
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
BHLHE40#8553326.92308812818640.0001069419523743840.00148918807520377
E2F4#187437.600836189170660.004354147360375710.0206466649793543
EBF1#187947.12517347725520.0007230531046774210.00576890322378955
GTF2B#2959212.77753197372970.00919936089559720.0347828561499991
IRF3#3661218.79278088459580.004339629777121510.0205843670766097
JUNB#3726212.24425306392850.009990490593345960.037464877812512
NFYB#4801310.05587595212190.001938165606725460.0113859870514569
POU2F2#545235.463674434645510.01115650094469780.040996931922286
RFX5#599337.228746496317060.00502918278958660.0234630046172445
SMARCB1#6598310.95162946869440.001511872848343180.00964972733655892
SP2#6668210.46141219753790.01353191183347140.0477726849871858
SREBF1#6720218.80233977619530.004335312729587370.0205751034338533



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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