Coexpression cluster:C1354

Full id: C1354_CD4_CD19_CD8_cord_Natural_Mast_thymus

Phase1 CAGE Peaks

Hg19::chr11:94227129..94227182,+	p1@ANKRD49
Hg19::chr19:21203451..21203475,+	p1@ZNF430
Hg19::chr19:21324829..21324855,+	p1@ZNF431
Hg19::chr4:56814968..56815018,+	p1@CEP135
Hg19::chr4:84376953..84377040,-	p1@HELQ
Hg19::chr7:86781734..86781777,+	p1@DMTF1

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0006355	regulation of transcription, DNA-dependent	0.0283845759598042
GO:0006351	transcription, DNA-dependent	0.0283845759598042
GO:0032774	RNA biosynthetic process	0.0283845759598042
GO:0003677	DNA binding	0.0283845759598042
GO:0045449	regulation of transcription	0.0283845759598042
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0283845759598042
GO:0006350	transcription	0.0283845759598042
GO:0010468	regulation of gene expression	0.0283845759598042
GO:0031323	regulation of cellular metabolic process	0.0283845759598042
GO:0019222	regulation of metabolic process	0.0283845759598042
GO:0016070	RNA metabolic process	0.0283845759598042
GO:0043229	intracellular organelle	0.0364791675777369
GO:0043226	organelle	0.0364791675777369
GO:0010467	gene expression	0.0463822808005125
GO:0005813	centrosome	0.0463822808005125
GO:0050794	regulation of cellular process	0.0463822808005125
GO:0005815	microtubule organizing center	0.0463822808005125
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0463822808005125
GO:0005634	nucleus	0.0473610801434053
GO:0050789	regulation of biological process	0.0473610801434053
GO:0044424	intracellular part	0.0473610801434053
GO:0003676	nucleic acid binding	0.0485494265355204

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	3.35e-56	168
angioblastic mesenchymal cell	3.35e-56	168
hematopoietic cell	4.02e-52	177
hematopoietic oligopotent progenitor cell	8.20e-52	161
hematopoietic multipotent progenitor cell	8.20e-52	161
leukocyte	2.32e-50	136
hematopoietic lineage restricted progenitor cell	8.23e-42	120
nongranular leukocyte	3.04e-39	115
myeloid cell	1.63e-28	108
common myeloid progenitor	1.63e-28	108
nucleate cell	6.12e-22	55
myeloid leukocyte	6.62e-22	72
lymphoid lineage restricted progenitor cell	3.50e-21	52
lymphocyte	4.01e-21	53
common lymphoid progenitor	4.01e-21	53
granulocyte monocyte progenitor cell	1.64e-19	67
myeloid lineage restricted progenitor cell	5.20e-19	66
macrophage dendritic cell progenitor	3.51e-17	61
monopoietic cell	3.03e-16	59
monocyte	3.03e-16	59
monoblast	3.03e-16	59
promonocyte	3.03e-16	59
classical monocyte	6.94e-16	42
CD14-positive, CD16-negative classical monocyte	6.94e-16	42
defensive cell	5.30e-15	48
phagocyte	5.30e-15	48
mature alpha-beta T cell	2.06e-11	18
alpha-beta T cell	2.06e-11	18
immature T cell	2.06e-11	18
mature T cell	2.06e-11	18
immature alpha-beta T cell	2.06e-11	18
T cell	7.19e-11	25
pro-T cell	7.19e-11	25
lymphocyte of B lineage	6.91e-10	24
pro-B cell	6.91e-10	24
B cell	1.10e-08	14
mesenchymal cell	1.81e-08	354
CD8-positive, alpha-beta T cell	3.90e-08	11
motile cell	1.68e-07	386
connective tissue cell	3.04e-07	361

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	4.96e-25	98
blood island	4.96e-25	98
hemolymphoid system	1.50e-21	108
bone marrow	2.93e-16	76
immune system	1.45e-15	93
bone element	1.08e-14	82
skeletal element	1.53e-12	90
skeletal system	1.59e-10	100
adult organism	2.25e-09	114
blood	7.75e-08	15
haemolymphatic fluid	7.75e-08	15
organism substance	7.75e-08	15
connective tissue	3.38e-07	371

Disease

Ontology term	p-value	n
hematologic cancer	6.02e-07	51
immune system cancer	6.02e-07	51

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

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
MA0003.1	0.176622
MA0004.1	0.558729
MA0006.1	1.79433
MA0007.1	0.539222
MA0009.1	1.03681
MA0014.1	0.108006
MA0017.1	0.432438
MA0019.1	0.7124
MA0024.1	2.14259
MA0025.1	1.17262
MA0027.1	2.65688
MA0028.1	2.77054
MA0029.1	0.949428
MA0030.1	0.937696
MA0031.1	0.871496
MA0038.1	1.59836
MA0040.1	0.955415
MA0041.1	0.578072
MA0042.1	0.544748
MA0043.1	1.03713
MA0046.1	1.02569
MA0048.1	0.906394
MA0050.1	0.545671
MA0051.1	0.661179
MA0052.1	0.959373
MA0055.1	0.465994
MA0056.1	0
MA0057.1	0.147053
MA0058.1	0.458909
MA0059.1	0.457555
MA0060.1	2.08473
MA0061.1	0.23892
MA0063.1	0
MA0066.1	1.59928
MA0067.1	1.35893
MA0068.1	0.199491
MA0069.1	1.02175
MA0070.1	1.01032
MA0071.1	0.625297
MA0072.1	1.00572
MA0073.1	0.0214749
MA0074.1	0.660398
MA0076.1	4.17659
MA0077.1	0.997832
MA0078.1	0.763954
MA0081.1	0.457725
MA0083.1	1.04447
MA0084.1	1.5477
MA0087.1	1.00322
MA0088.1	0.32124
MA0089.1	0
MA0090.1	0.490736
MA0091.1	1.37996
MA0092.1	0.522012
MA0093.1	1.02138
MA0095.1	0
MA0098.1	0
MA0100.1	0.679972
MA0101.1	0.397846
MA0103.1	0.381434
MA0105.1	0.134725
MA0106.1	0.70837
MA0107.1	0.320267
MA0108.2	0.868347
MA0109.1	0
MA0111.1	0.504913
MA0113.1	0.725375
MA0114.1	0.845337
MA0115.1	1.28169
MA0116.1	0.323925
MA0117.1	1.07516
MA0119.1	0.440684
MA0122.1	1.10154
MA0124.1	1.23968
MA0125.1	1.15445
MA0130.1	0
MA0131.1	0.782708
MA0132.1	0
MA0133.1	0
MA0135.1	1.06778
MA0136.1	0.672893
MA0139.1	0.226048
MA0140.1	0.622527
MA0141.1	0.455728
MA0142.1	0.838805
MA0143.1	0.725558
MA0144.1	1.47313
MA0145.1	0.347815
MA0146.1	0.718193
MA0147.1	0.87383
MA0148.1	0.584698
MA0149.1	0.612449
MA0062.2	4.43009
MA0035.2	0.621793
MA0039.2	0.569061
MA0138.2	0.765223
MA0002.2	1.3092
MA0137.2	1.06611
MA0104.2	0.26661
MA0047.2	0.695777
MA0112.2	0.680553
MA0065.2	0.718489
MA0150.1	0.484557
MA0151.1	0
MA0152.1	0.629368
MA0153.1	1.13732
MA0154.1	0.413181
MA0155.1	0.318517
MA0156.1	1.07131
MA0157.1	0.810597
MA0158.1	0
MA0159.1	0.875329
MA0160.1	0.600559
MA0161.1	0
MA0162.1	0.150673
MA0163.1	0.0270301
MA0164.1	0.738243
MA0080.2	0.394469
MA0018.2	0.709805
MA0099.2	0.629739
MA0079.2	0.0318308
MA0102.2	1.58513
MA0258.1	0.788656
MA0259.1	0.893594
MA0442.1	0

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

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CHD2#1106	5	8.62001902843071	4.6560374997265e-05	0.000814798760780724
E2F4#1874	5	10.5567169294037	1.71705502564041e-05	0.000392573357755821
ELF1#1997	6	4.25809795880754	0.000167722477628883	0.0020513839841999
ELK4#2005	4	10.823787772312	0.000195059997301046	0.00234888401454214
GABPB1#2553	6	7.06768383618217	8.01905956107035e-06	0.000222799298084232
GTF2F1#2962	3	6.36983043837883	0.00806820819630316	0.0319143883579027
HEY1#23462	6	4.04011104310571	0.000229896855580751	0.00252951935313928
IRF1#3659	5	6.36430312796992	0.00020566751420509	0.00243865911853604
IRF3#3661	3	23.4909761057448	0.000183647351499455	0.0022235040277361
MAX#4149	4	4.30170367267141	0.00664492391067637	0.0282937544156527
MXI1#4601	4	6.6410477525062	0.00128851695803914	0.00863744689221113
NFKB1#4790	5	4.5733861868282	0.0010219625937113	0.00724348498979396
NFYA#4800	3	9.21279034991526	0.00282275556436427	0.0154486070526982
NFYB#4801	4	11.1731955023576	0.000172334334821877	0.00209918656338489
PAX5#5079	4	4.44637702078522	0.00587473351924079	0.0263586928734798
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380024774861801
RFX5#5993	5	10.0399256893292	2.19894173045095e-05	0.000482570446284023
SIN3A#25942	6	5.40888472681514	3.99207083571449e-05	0.000742392959421627
SP1#6667	4	3.7989209187606	0.0105224661679851	0.0389410667275501
SP2#6668	3	13.0767652469223	0.00102434039793732	0.00725886055232567
SPI1#6688	4	5.46954900568182	0.0026973005361414	0.0148413345289538
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00572729233453074
TAF7#6879	5	9.5275578374366	2.84599232912077e-05	0.000599742923448435
TBP#6908	6	3.70677068709639	0.00038541647290796	0.00377532461208352
TCF12#6938	5	8.86205408515535	4.06365504449859e-05	0.000743264569513815
TCF7L2#6934	5	8.97514713594779	3.818060286338e-05	0.000719773282030424
ZBTB33#10009	2	10.5549083433271	0.0137425073714059	0.048380426325162
ZEB1#6935	3	8.44421600877193	0.00362384381073359	0.0183349783814168

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

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This analysis result is provided for C0 - C305 clusters.