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Coexpression cluster:C473: Difference between revisions

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

Latest revision as of 11:23, 17 September 2013


Full id: C473_immature_Eosinophils_cord_CD14_CD4_CD8_Natural



Phase1 CAGE Peaks

Hg19::chr10:106028656..106028685,-p1@MIR4482-1
Hg19::chr10:3827776..3827787,+p@chr10:3827776..3827787
+
Hg19::chr11:18548217..18548243,+p@chr11:18548217..18548243
+
Hg19::chr11:58346354..58346370,-p@chr11:58346354..58346370
-
Hg19::chr12:25539298..25539317,+p@chr12:25539298..25539317
+
Hg19::chr13:45151945..45151990,-p@chr13:45151945..45151990
-
Hg19::chr14:24583688..24583704,-p@chr14:24583688..24583704
-
Hg19::chr16:20912197..20912222,-p4@DCUN1D3
Hg19::chr19:49376263..49376332,-p@chr19:49376263..49376332
-
Hg19::chr1:171455122..171455146,-p1@BC007549
Hg19::chr2:96811170..96811186,-p1@DUSP2
Hg19::chr3:150126416..150126437,+p3@TSC22D2
Hg19::chr3:5020939..5020952,+p2@BHLHE40
Hg19::chr4:103461950..103461953,+p@chr4:103461950..103461953
+
Hg19::chr6:108879688..108879712,-p@chr6:108879688..108879712
-
Hg19::chr7:151216229..151216250,+p@chr7:151216229..151216250
+
Hg19::chr7:73508557..73508570,-p@chr7:73508557..73508570
-
Hg19::chr8:102218439..102218455,-p3@ZNF706
Hg19::chr8:81397846..81397860,+p3@ZBTB10
Hg19::chr8:81397876..81397898,+p5@ZBTB10


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:0051019mitogen-activated protein kinase binding0.0135982338777593
GO:0008330protein tyrosine/threonine phosphatase activity0.0135982338777593
GO:0033549MAP kinase phosphatase activity0.0326141514013656
GO:0017017MAP kinase tyrosine/serine/threonine phosphatase activity0.0326141514013656
GO:0000188inactivation of MAPK activity0.0326141514013656
GO:0043407negative regulation of MAP kinase activity0.0362283455576895



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
leukocyte4.38e-68136
hematopoietic stem cell1.08e-54168
angioblastic mesenchymal cell1.08e-54168
nongranular leukocyte4.32e-52115
hematopoietic lineage restricted progenitor cell1.86e-51120
hematopoietic cell7.48e-51177
hematopoietic oligopotent progenitor cell5.70e-49161
hematopoietic multipotent progenitor cell5.70e-49161
classical monocyte3.05e-3542
CD14-positive, CD16-negative classical monocyte3.05e-3542
myeloid leukocyte5.67e-3072
defensive cell1.18e-2848
phagocyte1.18e-2848
lymphocyte8.77e-2753
common lymphoid progenitor8.77e-2753
lymphoid lineage restricted progenitor cell2.56e-2652
granulocyte monocyte progenitor cell6.94e-2667
nucleate cell3.53e-2555
macrophage dendritic cell progenitor2.70e-2361
myeloid lineage restricted progenitor cell2.01e-2266
myeloid cell5.46e-22108
common myeloid progenitor5.46e-22108
monopoietic cell9.94e-2259
monocyte9.94e-2259
monoblast9.94e-2259
promonocyte9.94e-2259
mesenchymal cell4.99e-19354
connective tissue cell7.89e-18361
motile cell3.28e-15386
T cell2.13e-1225
pro-T cell2.13e-1225
lymphocyte of B lineage2.21e-1224
pro-B cell2.21e-1224
mature alpha-beta T cell3.29e-1218
alpha-beta T cell3.29e-1218
immature T cell3.29e-1218
mature T cell3.29e-1218
immature alpha-beta T cell3.29e-1218
stuff accumulating cell6.49e-1287
B cell2.28e-1014
multi fate stem cell7.99e-10427
stem cell1.24e-09441
somatic stem cell3.51e-09433
intermediate monocyte9.07e-099
CD14-positive, CD16-positive monocyte9.07e-099
granulocyte2.83e-088
CD8-positive, alpha-beta T cell4.36e-0711
CD4-positive, alpha-beta T cell9.82e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.08e-2398
blood island1.08e-2398
bone marrow1.14e-2276
bone element2.40e-2182
hemolymphoid system4.56e-20108
immune system4.45e-1993
skeletal element3.59e-1790
connective tissue9.97e-17371
skeletal system2.31e-14100


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)
MA0003.13.96154
MA0004.11.61762
MA0006.11.49379
MA0007.10.168078
MA0009.10.561062
MA0014.11.7317
MA0017.10.105116
MA0019.10.290278
MA0024.10.467291
MA0025.10.684106
MA0027.12.13512
MA0028.10.308337
MA0029.10.484339
MA0030.10.474212
MA0031.10.41796
MA0038.10.25521
MA0040.10.489524
MA0041.10.193578
MA0042.10.171628
MA0043.11.37972
MA0046.10.551181
MA0048.10.650948
MA0050.10.512765
MA0051.10.251994
MA0052.10.492957
MA0055.10.271837
MA0056.10
MA0057.11.21384
MA0058.11.81788
MA0059.10.378591
MA0060.12.28245
MA0061.10.490814
MA0063.10
MA0066.10.710255
MA0067.10.858361
MA0068.10.370416
MA0069.10.547689
MA0070.10.537571
MA0071.10.641904
MA0072.10.533514
MA0073.14.07757
MA0074.10.70075
MA0076.10.805991
MA0077.10.526569
MA0078.10.33032
MA0081.10.118989
MA0083.10.567893
MA0084.11.03923
MA0087.10.531309
MA0088.10.535351
MA0089.10
MA0090.10.138104
MA0091.10.182521
MA0092.10.157193
MA0093.12.07238
MA0095.10
MA0098.10
MA0100.10.265855
MA0101.11.52548
MA0103.10.27232
MA0105.12.2413
MA0106.10.28721
MA0107.11.15991
MA0108.20.415325
MA0109.10
MA0111.10.146643
MA0113.10.300221
MA0114.10.0506063
MA0115.10.785493
MA0116.10.199654
MA0117.10.595385
MA0119.10.354175
MA0122.10.619196
MA0124.10.746208
MA0125.10.667416
MA0130.10
MA0131.13.4014
MA0132.10
MA0133.10
MA0135.10.588754
MA0136.10.260607
MA0139.10.450711
MA0140.10.637307
MA0141.10.117869
MA0142.10.39079
MA0143.10.300362
MA0144.10.0449457
MA0145.10.402421
MA0146.10.166442
MA0147.11.6733
MA0148.10.198049
MA0149.10.21714
MA0062.20.473404
MA0035.20.223695
MA0039.21.87696
MA0138.21.5856
MA0002.20.0300734
MA0137.20.317751
MA0104.21.7673
MA0047.20.761085
MA0112.20.800042
MA0065.20.133665
MA0150.10.134443
MA0151.10
MA0152.10.229055
MA0153.10.65174
MA0154.10.337609
MA0155.11.01632
MA0156.10.0971366
MA0157.10.367703
MA0158.10
MA0159.10.204897
MA0160.10.20889
MA0161.10
MA0162.11.66396
MA0163.10.228682
MA0164.10.834714
MA0080.20.289769
MA0018.20.288301
MA0099.21.21192
MA0079.26.21017
MA0102.21.07547
MA0258.10.366495
MA0259.11.23558
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#8553511.21795338674446.42747363862819e-050.00104593162877016
CCNT2#905103.168100788481320.0003803542932567060.00376600512262392
CEBPB#1051114.384131194203656.79503322842392e-060.000197678683939656
CHD2#110663.103206850235060.009578837412862720.0360544996057941
E2F1#1869133.189802989671561.87417375144146e-050.000425422369977818
E2F6#1876102.508577865848690.002524731868879820.0139972646594086
EGR1#1958102.494089547405070.00264189150021730.014594895868352
ELF1#1997132.76776367322499.22980427778795e-050.00134329923211803
EP300#203393.048273776800440.001181284506666370.00801482313985114
FOS#235394.049079889002480.0001371204655711730.00179210665796367
FOSL2#235554.232550151140420.005268996048930470.0244041278262561
FOXA1#316963.324425924815640.006875001937886880.0291167204943621
FOXA2#317067.389139125799570.000105831675770420.0014753009057377
GABPB1#255382.827073534472870.004105195986104440.0195674576054384
GATA3#262545.44730327144120.005486793888199380.0248454416792254
GTF2F1#296263.82189826302730.003453000158379710.0175513643617569
HEY1#23462153.030083282329283.32829050484245e-060.000111197483056699
HMGN3#932493.680346475507770.0002868471216799290.00304947338570135
IRF1#365983.054865501425560.00250226972055260.0140351529186248
IRF3#366137.047292831723440.008377527503002730.0329222078147992
JUN#372563.75384875770090.003777848601605140.0186621289425333
MAX#414992.903649979053210.001684679633019630.0105293989343469
MEF2A#420576.560130818375425.13114917567969e-050.000873499737178176
MEF2C#420836.19670317389360.01187407979154320.0432412922120358
MXI1#460194.482707232941686.16323643311231e-050.00101017302234435
MYC#4609123.133369122965646.50448960500582e-050.00105648894223515
NFKB1#4790174.664853910564761.73611812252636e-101.8186403269662e-08
NFYA#480054.606395174957630.003669499074231540.0185237959211981
NFYB#480154.189948313384110.005499829294076840.0249012299667964
PAX5#5079103.334782765588910.0002472398777180710.00268582125951712
POLR2A#5430181.932707858902266.29675214552603e-050.00102802328798905
POU2F2#5452104.553062028871261.65166365444159e-050.000381127044644776
REST#597883.860011486451210.0005295700026501390.00457807809840061
RFX5#599384.819164330878040.0001135990070785040.00155575225547756
SIN3A#25942143.786219308770596.7895687647145e-073.07233870111793e-05
SMARCB1#659865.475814734347220.0005365334762243630.00463597416425881
SP2#666845.230706098768930.00632830151783790.0275579152825532
SPI1#668872.871513227982950.007285172039470230.0301400761618694
STAT1#677255.17664687429980.002209802268842530.012726896391069
TAF1#6872152.507284714308974.1297690460894e-050.000749972090774701
TAF7#687963.429920821477170.005903378583414720.0264803915248572
TBP#6908162.965416549677111.18297025119262e-064.81857371545654e-05
TCF12#693873.722062715765250.001666859736874120.0104217650897627
TCF7L2#693473.769561797098070.001547352602133020.00983471022481564
TFAP2A#702064.955590311913490.0009093672692604040.00661881721613265
TFAP2C#702284.323691443944090.0002427975840692140.00264085991278949
USF1#7391113.498824602464386.03444132472198e-050.000990929272818614
USF2#739274.547269084774360.0005040821561941330.00444156216238582
YY1#7528112.701143912419620.0006614778782913620.00541453782670049
ZBTB33#1000969.499417508994352.61702144212769e-050.000564126114333072
ZBTB7A#5134172.573168257756560.01317328582501380.0466137488828941



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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