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Coexpression cluster:C871: Difference between revisions

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{{Coexpression_clusters
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.1;0.474342,MA0141.1;0.322254,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;2.35887,MA0145.1;0.046841,MA0146.1;0.175555,MA0147.1;0.607251,MA0148.1;0.439278,MA0149.1;0.464973,MA0062.2;0.421263,MA0035.2;0.473658,MA0039.2;1.46687,MA0138.2;0.608783,MA0002.2;0.46405,MA0137.2;0.780538,MA0104.2;0.486672,MA0047.2;0.542971,MA0112.2;0.166662,MA0065.2;0.719797,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;0.225151,MA0155.1;0.156896,MA0156.1;0.785298,MA0157.1;0.652111,MA0158.1;0,MA0159.1;0.60858,MA0160.1;0.453945,MA0161.1;0,MA0162.1;0.767014,MA0163.1;1.18882,MA0164.1;1.42569,MA0080.2;1.35856,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;1.87627,MA0102.2;1.41188,MA0258.1;0.180288,MA0259.1;0.624802,MA0442.1;0}}
|full_id=C871_CD19_Mast_CD4_CD8_Natural_Peripheral_Basophils
|id=C871
}}

Latest revision as of 11:32, 17 September 2013


Full id: C871_CD19_Mast_CD4_CD8_Natural_Peripheral_Basophils



Phase1 CAGE Peaks

Hg19::chr10:27531947..27531980,-p@chr10:27531947..27531980
-
Hg19::chr15:52471650..52471680,+p@chr15:52471650..52471680
+
Hg19::chr1:231473624..231473639,-p2@EXOC8
Hg19::chr1:31191601..31191660,+p1@LOC100129196
Hg19::chr2:202123066..202123088,-p@chr2:202123066..202123088
-
Hg19::chr4:40198642..40198689,+p1@RHOH
Hg19::chr5:43484423..43484517,-p2@C5orf28
Hg19::chr8:41998304..41998320,-p@chr8:41998304..41998320
-
Hg19::chr9:6757183..6757204,+p9@KDM4C


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:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.0384038116999737
GO:0005095GTPase inhibitor activity0.0384038116999737



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
leukocyte1.45e-40136
hematopoietic stem cell2.64e-40168
angioblastic mesenchymal cell2.64e-40168
hematopoietic cell6.23e-37177
hematopoietic oligopotent progenitor cell1.07e-35161
hematopoietic multipotent progenitor cell1.07e-35161
hematopoietic lineage restricted progenitor cell7.45e-33120
nucleate cell8.92e-3355
lymphocyte9.33e-3253
common lymphoid progenitor9.33e-3253
lymphoid lineage restricted progenitor cell1.16e-3152
nongranular leukocyte3.17e-30115
T cell2.66e-1525
pro-T cell2.66e-1525
lymphocyte of B lineage4.10e-1524
pro-B cell4.10e-1524
mature alpha-beta T cell3.29e-1418
alpha-beta T cell3.29e-1418
immature T cell3.29e-1418
mature T cell3.29e-1418
immature alpha-beta T cell3.29e-1418
B cell1.36e-1114
myeloid cell3.01e-10108
common myeloid progenitor3.01e-10108
CD8-positive, alpha-beta T cell2.31e-0911
myeloid leukocyte2.02e-0872
granulocyte monocyte progenitor cell5.55e-0767
intermediate monocyte8.06e-079
CD14-positive, CD16-positive monocyte8.06e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.17e-1398
blood island5.17e-1398
adult organism2.28e-12114
hemolymphoid system8.52e-12108
blood3.65e-0915
haemolymphatic fluid3.65e-0915
organism substance3.65e-0915
immune system9.93e-0793


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)
MA0003.10.0913842
MA0004.11.06719
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.11.14942
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.11.84783
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.264106
MA0050.11.04113
MA0051.10.510444
MA0052.10.795605
MA0055.10.088427
MA0056.10
MA0057.10.253359
MA0058.10.325084
MA0059.10.865474
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.354973
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.11.21679
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.865814
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.158781
MA0089.10
MA0090.10.931587
MA0091.10.417885
MA0092.10.381858
MA0093.10.73976
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.582067
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.83188
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.808973
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.12.35887
MA0145.10.046841
MA0146.10.175555
MA0147.10.607251
MA0148.10.439278
MA0149.10.464973
MA0062.20.421263
MA0035.20.473658
MA0039.21.46687
MA0138.20.608783
MA0002.20.46405
MA0137.20.780538
MA0104.20.486672
MA0047.20.542971
MA0112.20.166662
MA0065.20.719797
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.225151
MA0155.10.156896
MA0156.10.785298
MA0157.10.652111
MA0158.10
MA0159.10.60858
MA0160.10.453945
MA0161.10
MA0162.10.767014
MA0163.11.18882
MA0164.11.42569
MA0080.21.35856
MA0018.20.556211
MA0099.20.481058
MA0079.21.87627
MA0102.21.41188
MA0258.10.180288
MA0259.10.624802
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
BRF2#552901119.3972868217050.008344470633487870.0328553503672324
E2F6#187673.902232235764630.0003067423599492730.00316153807665471
ELF1#199773.311853967961420.0008960205810173620.00666853085305154
GTF2F1#296245.662071500781180.00346420020706550.0176014403028807
HEY1#2346262.693407362070470.009487643473762270.0357421634295083
IRF4#366237.304837562248040.006482999615409630.0281459094127771
MAX#414975.018654284783325.77474544696214e-050.000962049194026605
MEF2A#420536.247743636548020.01000005008462560.0374966872792234
MXI1#460144.427365168337470.008444657415134930.0327765562575917
MYC#460984.642028330319471.34916872863392e-050.000327155404805661
NFKB1#479063.658708949462560.001850649648602720.0109327449884281
POLR2A#543092.147453176558070.001029412892608020.00728343967827989
POU2F2#545266.070749371828350.0001095272295875280.00152356344311292
SIN3A#2594274.206910343078440.0001867843656174470.00225991338747922
SMC3#912646.686636819970150.001873161593351730.0110420005445652
TAF1#687293.343046285745291.91655056102793e-050.000433346230879403
TBP#690872.883043867741630.002187802002126050.0126147989455111
TCF12#693844.726428845416190.006680355302603970.0284179718727814
YY1#752873.819799472108550.0003529672812141940.00353539367821322



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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