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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:25, 17 September 2013


Full id: C554_Mast_Natural_CD8_CD14_CD4_Basophils_CD34



Phase1 CAGE Peaks

Hg19::chr10:3852591..3852602,-p@chr10:3852591..3852602
-
Hg19::chr10:3934581..3934590,-p@chr10:3934581..3934590
-
Hg19::chr17:7746197..7746211,+p@chr17:7746197..7746211
+
Hg19::chr18:2972215..2972224,-p@chr18:2972215..2972224
-
Hg19::chr19:40502828..40502848,-p@chr19:40502828..40502848
-
Hg19::chr1:156076015..156076041,-p@chr1:156076015..156076041
-
Hg19::chr1:156083971..156084011,-p@chr1:156083971..156084011
-
Hg19::chr1:156084289..156084307,-p@chr1:156084289..156084307
-
Hg19::chr1:59250073..59250095,+p@chr1:59250073..59250095
+
Hg19::chr20:24930639..24930652,+p@chr20:24930639..24930652
+
Hg19::chr22:39548943..39548962,+p@chr22:39548943..39548962
+
Hg19::chr2:225906150..225906177,-p@chr2:225906150..225906177
-
Hg19::chr5:130600546..130600567,-p@chr5:130600546..130600567
-
Hg19::chr7:157069496..157069512,-p@chr7:157069496..157069512
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Hg19::chr8:38644503..38644535,-p@chr8:38644503..38644535
-
Hg19::chr9:136017930..136017940,+p@chr9:136017930..136017940
+


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
classical monocyte2.49e-7142
CD14-positive, CD16-negative classical monocyte2.49e-7142
leukocyte3.12e-68136
defensive cell4.86e-6148
phagocyte4.86e-6148
hematopoietic lineage restricted progenitor cell6.85e-59120
nongranular leukocyte8.86e-57115
granulocyte monocyte progenitor cell4.90e-5467
hematopoietic stem cell5.06e-54168
angioblastic mesenchymal cell5.06e-54168
myeloid leukocyte1.06e-5272
hematopoietic cell2.36e-52177
macrophage dendritic cell progenitor1.85e-5061
myeloid lineage restricted progenitor cell2.68e-4966
hematopoietic oligopotent progenitor cell2.51e-47161
hematopoietic multipotent progenitor cell2.51e-47161
monopoietic cell1.19e-4659
monocyte1.19e-4659
monoblast1.19e-4659
promonocyte1.19e-4659
myeloid cell1.29e-36108
common myeloid progenitor1.29e-36108
stuff accumulating cell1.21e-3087
mesenchymal cell1.82e-18354
connective tissue cell8.85e-18361
intermediate monocyte5.88e-179
CD14-positive, CD16-positive monocyte5.88e-179
motile cell2.29e-15386
multi fate stem cell4.43e-13427
stem cell7.02e-13441
somatic stem cell1.15e-12433
CD4-positive, alpha-beta T cell1.06e-106
mature alpha-beta T cell3.53e-1018
alpha-beta T cell3.53e-1018
immature T cell3.53e-1018
mature T cell3.53e-1018
immature alpha-beta T cell3.53e-1018
lymphoid lineage restricted progenitor cell3.92e-1052
lymphocyte7.34e-1053
common lymphoid progenitor7.34e-1053
natural killer cell2.13e-093
pro-NK cell2.13e-093
nucleate cell2.40e-0955
basophil5.96e-093
T cell2.54e-0825
pro-T cell2.54e-0825
single nucleate cell2.61e-083
mononuclear cell2.61e-083
circulating cell4.96e-076
Uber Anatomy
Ontology termp-valuen
bone marrow8.01e-4976
hematopoietic system4.86e-4898
blood island4.86e-4898
bone element2.12e-4482
hemolymphoid system2.79e-44108
immune system6.45e-4493
skeletal element2.05e-3990
skeletal system2.64e-34100
musculoskeletal system6.64e-17167
connective tissue7.63e-17371
lateral plate mesoderm1.68e-16203
mesoderm5.79e-08315
mesoderm-derived structure5.79e-08315
presumptive mesoderm5.79e-08315


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)
MA0003.10.357653
MA0004.10.238283
MA0006.10.392773
MA0007.10.636564
MA0009.10.644692
MA0014.10.446753
MA0017.10.89607
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.419336
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.10.644989
MA0046.10.634468
MA0048.10.201309
MA0050.10.647665
MA0051.10.317617
MA0052.10.574006
MA0055.10.324189
MA0056.10
MA0057.10.615711
MA0058.10.167587
MA0059.10.166682
MA0060.10.212419
MA0061.13.20126
MA0063.10
MA0066.10.860141
MA0067.10.948938
MA0068.10.303278
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.10.72364
MA0074.10.850035
MA0076.10.528959
MA0077.10.608956
MA0078.10.402443
MA0081.10.499456
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.0965118
MA0089.10
MA0090.10.189305
MA0091.10.240316
MA0092.10.211423
MA0093.10.397767
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.12.55174
MA0103.10.118522
MA0105.12.96806
MA0106.10.355999
MA0107.12.67757
MA0108.20.492699
MA0109.10
MA0111.10.578093
MA0113.10.370073
MA0114.11.46864
MA0115.10.874839
MA0116.10.607827
MA0117.10.680135
MA0119.10.155538
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.87256
MA0139.10.0410754
MA0140.10.7823
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.11.39182
MA0145.10.113672
MA0146.10.0427873
MA0147.10.296651
MA0148.10.257816
MA0149.10.279141
MA0062.20.382208
MA0035.20.780994
MA0039.20.899284
MA0138.20.403517
MA0002.20.760603
MA0137.20.848496
MA0104.20.211351
MA0047.20.345656
MA0112.20.390337
MA0065.22.54623
MA0150.10.5439
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.11.15225
MA0155.10.204406
MA0156.10.854962
MA0157.10.442323
MA0158.10
MA0159.10.29763
MA0160.10.26995
MA0161.10
MA0162.10.467716
MA0163.10.864319
MA0164.12.64221
MA0080.21.87465
MA0018.20.357181
MA0099.21.44708
MA0079.21.51462
MA0102.21.16862
MA0258.10.520754
MA0259.10.309645
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
BCL11A#5333558.86545471987720.0001712746542035670.00208895873062786
EGR1#195882.494089547405070.0071065613147760.029627645888543
FOS#235373.93660544764130.0009600132569505240.00690658018479409
FOSL1#806137.446296196819940.006988269650209680.0295389304677938
FOSL2#235555.290687688925530.001809065771084470.0109414535595489
JUN#372564.692310947126130.001030862620745210.00729221493145552
MAX#414972.822993035190620.00671495219734910.0285430562693912
MEF2A#420544.685807727411010.008783099930456450.0333623631073628
MXI1#460163.735589360784740.00336025903705470.0173304737565904
NFKB1#479082.744031712096920.003856163139355890.0190237988715725
PAX5#507983.334782765588910.001055267737319320.00745677315411991
POU2F2#545273.983929275262350.0008930219510760040.00664763503552579
SMARCA4#6597219.5957379134860.004597623869893720.0217262223133718
SMARCC1#659938.18687987243090.005376255197450410.0246971944828029
SRF#672254.311618206927440.004430314153512830.0209735542304849
STAT1#677256.470808592874750.0007317668712721070.00582729700867614
STAT3#677463.944799373932840.002544236462237630.0140867047595629
TAF1#6872122.507284714308970.0002576836954007160.00276419756203321
TBP#6908112.548404847378770.0005856282752669240.00490633975939373
TCF12#693863.987924338319910.002406057678715160.0135661749126671
TCF7L2#693453.365680175980420.01257049842947540.0454603790115996



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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