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Coexpression cluster:C972: Difference between revisions

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{{Coexpression_clusters
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guanylyltransferase activity!0.0100778500780597!8732$GO:0004651!polynucleotide 5'-phosphatase activity!0.0100778500780597!8732$GO:0019204!nucleotide phosphatase activity!0.0100778500780597!8732$GO:0009452!RNA capping!0.0100778500780597!8732$GO:0006370!mRNA capping!0.0100778500780597!8732$GO:0008192!RNA guanylyltransferase activity!0.0125960147274817!8732$GO:0006397!mRNA processing!0.0266730623567725!8732;55119$GO:0016071!mRNA metabolic process!0.0363574422340447!8732;55119$GO:0010467!gene 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|full_id=C972_granulocyte_CD4_CD19_Neutrophils_acute_CD8_Eosinophils
|id=C972
}}

Latest revision as of 11:34, 17 September 2013


Full id: C972_granulocyte_CD4_CD19_Neutrophils_acute_CD8_Eosinophils



Phase1 CAGE Peaks

Hg19::chr10:127408263..127408308,+p1@C10orf137
Hg19::chr11:47788847..47788919,-p1@FNBP4
Hg19::chr18:59854480..59854551,+p1@KIAA1468
Hg19::chr1:109234907..109234996,+p1@PRPF38B
Hg19::chr2:32582184..32582301,+p1@BIRC6
Hg19::chr3:101395963..101395993,-p1@ZBTB11
Hg19::chr6:64345698..64345750,+p2@PHF3
Hg19::chr6:89673299..89673349,-p1@RNGTT


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:0004484mRNA guanylyltransferase activity0.0100778500780597
GO:0004651polynucleotide 5'-phosphatase activity0.0100778500780597
GO:0019204nucleotide phosphatase activity0.0100778500780597
GO:0009452RNA capping0.0100778500780597
GO:0006370mRNA capping0.0100778500780597
GO:0008192RNA guanylyltransferase activity0.0125960147274817
GO:0006397mRNA processing0.0266730623567725
GO:0016071mRNA metabolic process0.0363574422340447
GO:0010467gene expression0.0461902140241185



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
hematopoietic stem cell9.56e-49168
angioblastic mesenchymal cell9.56e-49168
hematopoietic oligopotent progenitor cell1.96e-44161
hematopoietic multipotent progenitor cell1.96e-44161
hematopoietic cell2.75e-44177
leukocyte3.66e-43136
hematopoietic lineage restricted progenitor cell1.44e-34120
nongranular leukocyte4.03e-33115
myeloid cell3.43e-24108
common myeloid progenitor3.43e-24108
myeloid leukocyte6.21e-1972
nucleate cell9.62e-1955
lymphocyte1.01e-1853
common lymphoid progenitor1.01e-1853
lymphoid lineage restricted progenitor cell1.10e-1852
granulocyte monocyte progenitor cell2.71e-1667
classical monocyte2.73e-1542
CD14-positive, CD16-negative classical monocyte2.73e-1542
myeloid lineage restricted progenitor cell5.91e-1566
macrophage dendritic cell progenitor8.32e-1461
monopoietic cell5.97e-1359
monocyte5.97e-1359
monoblast5.97e-1359
promonocyte5.97e-1359
defensive cell1.22e-1248
phagocyte1.22e-1248
mature alpha-beta T cell6.01e-1118
alpha-beta T cell6.01e-1118
immature T cell6.01e-1118
mature T cell6.01e-1118
immature alpha-beta T cell6.01e-1118
T cell6.28e-1025
pro-T cell6.28e-1025
lymphocyte of B lineage2.83e-0824
pro-B cell2.83e-0824
CD8-positive, alpha-beta T cell1.01e-0711
B cell1.28e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.01e-1998
blood island1.01e-1998
hemolymphoid system2.05e-16108
bone marrow1.53e-1276
bone element2.04e-1282
immune system1.55e-1193
adult organism1.99e-11114
skeletal element9.45e-0990
skeletal system3.27e-07100
blood5.86e-0715
haemolymphatic fluid5.86e-0715
organism substance5.86e-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)
MA0003.11.34332
MA0004.11.15451
MA0006.11.47431
MA0007.10.437331
MA0009.10.918715
MA0014.12.6969
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.11.52958
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.11.12793
MA0051.10.553205
MA0052.10.842664
MA0055.11.64271
MA0056.10
MA0057.10.632427
MA0058.10.950944
MA0059.10.361075
MA0060.12.3723
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.823119
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.131075
MA0074.10.552456
MA0076.12.62795
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.11.17773
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.818737
MA0095.10
MA0098.10
MA0100.11.40058
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.655057
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.916926
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.11.17059
MA0145.10.830366
MA0146.10.934908
MA0147.11.95811
MA0148.10.480298
MA0149.10.506665
MA0062.22.15478
MA0035.20.515566
MA0039.22.57832
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.22.36725
MA0047.20.586412
MA0112.20.0572179
MA0065.20.844872
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.43752
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.11.29519
MA0163.11.06699
MA0164.10.627336
MA0080.20.303167
MA0018.21.46097
MA0099.20.523145
MA0079.22.23097
MA0102.21.46209
MA0258.10.209744
MA0259.11.29349
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#8553211.21795338674440.0127147255611290.0458691959543608
BRCA1#672512.61514415201491.47177326411908e-050.000349500973013489
CCNT2#90575.54417637984231.68072647241023e-050.000387234485003425
CEBPB#105143.985573812912410.01139163688734390.0417449531535897
CHD2#110656.465014271323040.0003676243258073190.00366113444864981
E2F1#186974.293965563019419.58670853279727e-050.00137079169284887
E2F4#187446.334030157642220.002095549459904640.0121203461285363
E2F6#187663.762866798773040.001207680027997810.0081875296620619
ELF1#199784.258097958807549.24826870984006e-060.000246649626094736
ELK4#2005612.1767612438511.37005744708648e-065.33311329542547e-05
ETS1#211356.080475576376460.0004913374346249240.0043922614341173
FOS#235344.49897765444720.007374489916227120.0304842411383671
GABPB1#255376.18422335665947.95182205325426e-060.000221284397394037
GTF2F1#296257.962288047973530.0001362053831339150.0017810384386031
HEY1#2346284.040111043105711.4081650274634e-050.00033941229472248
HMGN3#932455.111592327094120.001109515975889930.00770918362091464
IRF1#365976.682518284368414.6709523292352e-060.000145144180396607
IRF3#3661317.61823207930860.0004979994386673570.00440133395743252
JUND#372754.371664963669390.002289022009366710.0129904455597593
MAX#414964.839416631755340.0002917504313705360.00309781652113739
MXI1#460156.225982267974560.0004393954903539430.00409476448800531
MYC#460963.916711403707050.0009649270569246440.00694001906880744
NFKB1#479064.116047568145380.0007299856589784310.00581666073381006
NFYA#480049.212790349915260.0005085231351680210.00445588117407609
NFYB#480148.379896626768230.0007296914029278550.00581653491301956
NR2C2#7182312.23047908946530.001436803769416480.00922357544250342
NRF1#489957.631424654819320.0001668882994718450.00204549314734655
PAX5#507954.168478456986140.002847508706107280.0154384551605222
POLR2A#543082.147453176558070.002210725788971910.0127294073588288
POU2F2#545266.829593043306894.02833503357943e-050.000738485663633495
RFX5#599357.529944266996940.000177917256858560.00215888235030221
SIN3A#2594274.732774135963244.948745034002e-050.000848116151306424
SIX5#14791248.54335767772950.000677999305962630.00546960988069142
SP1#666753.561488361338060.005813761866596070.0261345274215739
SP2#666839.807573935191740.002707184665085610.0148894443750001
TAF1#687283.343046285745296.40776711117462e-050.00104435204326462
TAF7#687957.145668378077450.0002284466637700410.00252020081519798
TBP#690873.243424351209340.0006354223620492050.00521351842800353
TFAP2A#702036.194487889891860.009861483862380290.037051606759835
TFAP2C#702245.404614304930110.003775146896547010.0186496649509708
YY1#752874.297274406122129.53674534900876e-050.00136495566329331
ZBTB33#10009311.87427188624290.001564551645953250.00992529972372663



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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