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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 11:30, 17 September 2013


Full id: C777_Neutrophils_Eosinophils_CD19_CD4_CD8_Whole_Natural



Phase1 CAGE Peaks

Hg19::chr10:104404775..104404890,+p2@TRIM8
Hg19::chr11:114271463..114271474,+p7@RBM7
Hg19::chr12:12849622..12849654,+p@chr12:12849622..12849654
+
Hg19::chr12:32112340..32112358,+p2@C12orf35
Hg19::chr12:32112527..32112546,+p4@C12orf35
Hg19::chr15:55611128..55611179,+p2@PIGB
Hg19::chr1:176176198..176176259,-p2@RFWD2
Hg19::chr22:40440804..40440859,+p1@TNRC6B
Hg19::chr3:141205852..141205929,+p1@RASA2
Hg19::chr6:159466042..159466066,-p2@TAGAP


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
leukocyte7.20e-49136
hematopoietic stem cell1.14e-46168
angioblastic mesenchymal cell1.14e-46168
hematopoietic oligopotent progenitor cell8.79e-43161
hematopoietic multipotent progenitor cell8.79e-43161
hematopoietic cell2.71e-42177
hematopoietic lineage restricted progenitor cell1.85e-39120
nongranular leukocyte1.44e-37115
nucleate cell6.22e-2255
lymphocyte3.12e-2153
common lymphoid progenitor3.12e-2153
myeloid leukocyte5.07e-2172
lymphoid lineage restricted progenitor cell5.09e-2152
myeloid cell6.93e-21108
common myeloid progenitor6.93e-21108
granulocyte monocyte progenitor cell1.43e-1767
myeloid lineage restricted progenitor cell3.47e-1766
classical monocyte5.78e-1742
CD14-positive, CD16-negative classical monocyte5.78e-1742
macrophage dendritic cell progenitor1.26e-1561
defensive cell5.03e-1548
phagocyte5.03e-1548
monopoietic cell9.64e-1559
monocyte9.64e-1559
monoblast9.64e-1559
promonocyte9.64e-1559
mature alpha-beta T cell7.97e-1218
alpha-beta T cell7.97e-1218
immature T cell7.97e-1218
mature T cell7.97e-1218
immature alpha-beta T cell7.97e-1218
T cell1.51e-1025
pro-T cell1.51e-1025
lymphocyte of B lineage5.77e-1024
pro-B cell5.77e-1024
B cell3.13e-0814
CD8-positive, alpha-beta T cell5.49e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.53e-2398
blood island6.53e-2398
hemolymphoid system1.84e-21108
adult organism7.49e-19114
immune system4.35e-1593
bone marrow7.11e-1476
bone element1.05e-1182
skeletal element1.02e-0990
blood1.66e-0815
haemolymphatic fluid1.66e-0815
organism substance1.66e-0815
skeletal system1.28e-07100


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)
MA0003.12.29363
MA0004.10.990587
MA0006.10.236135
MA0007.10.952442
MA0009.10.828613
MA0014.12.41596
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.11.29053
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.11.02846
MA0042.10.963243
MA0043.10.828925
MA0046.10.817858
MA0048.10.220931
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.344701
MA0056.10
MA0057.10.46253
MA0058.10.293055
MA0059.10.291897
MA0060.11.97862
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.11.05557
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.431725
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.126492
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.11.2478
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.678051
MA0103.10.228129
MA0105.10.189717
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.536665
MA0117.10.865782
MA0119.11.39199
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.716757
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.14293
MA0146.13.10317
MA0147.11.03863
MA0148.10.403564
MA0149.10.428597
MA0062.21.21406
MA0035.20.437071
MA0039.21.78461
MA0138.20.569505
MA0002.20.129981
MA0137.20.255808
MA0104.20.845907
MA0047.20.504873
MA0112.20.133417
MA0065.20.147044
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.729959
MA0155.10.296882
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.11.23231
MA0163.10.990939
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.21.03243
MA0102.21.36707
MA0258.10.155735
MA0259.11.68088
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
CTBP2#1488212.54340006786560.01050432187371690.0388945923622321
E2F1#186973.435172450415530.0009731854789143080.00699556185782445
E2F6#187694.515440158527654.07099158370721e-060.000129506637225342
EGR1#195862.992907456886080.006446587185075730.0280076175806866
ELF1#199793.832288162926781.71269377095518e-050.00039191942319191
GATA1#262345.424123257520180.004321563399478210.0205163761933772
HEY1#2346283.232088834484570.0003859230867685430.00377745278903653
MYC#460973.655597310126580.000654500840128410.00535952746135887
NFKB1#479073.841644396935680.0004759144006094030.00433641808456163
PAX5#507964.00173931870670.001379489661762990.008985438492258
POLR2A#5430102.147453176558070.0004793377491637920.00436342327071536
POU2F2#545265.463674434645510.0002482209573289410.00267781722574912
REST#597865.790017229676810.0001793585011357230.00217510711798814
SIN3A#2594294.867996254133622.10202316614545e-067.66526527405952e-05
TAF1#6872103.343046285745295.73229241267096e-060.00017233013450977
TBP#6908103.706770687096392.04059382584877e-067.45166358663707e-05
TCF7L2#693444.308070625254940.009860462317564680.0370504343941046
YY1#752883.928936599883088.91962924709433e-050.00130616539391094
ZBTB7A#5134153.675954653937950.00645854601955880.0280490721780066



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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