Coexpression cluster:C1381

Full id: C1381_corpus_thyroid_cerebellum_pineal_thalamus_pituitary_substantia

Phase1 CAGE Peaks

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Hg19::chr13:41495851..41495883,-	p1@SUGT1P3
Hg19::chr19:40502938..40502987,+	p1@ZNF546
Hg19::chr22:38577782..38577858,-	p1@PLA2G6
Hg19::chr2:203776982..203777014,+	p1@ALS2CR8
Hg19::chr2:232646379..232646423,+	p3@COPS7B
Hg19::chr4:74124877..74124918,+	p1@ENST00000502790
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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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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>

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Cell Type

Ontology term	p-value	n
nucleate cell	1.45e-11	55
lymphoid lineage restricted progenitor cell	2.91e-11	52
lymphocyte	2.99e-11	53
common lymphoid progenitor	2.99e-11	53
mature alpha-beta T cell	2.95e-08	18
alpha-beta T cell	2.95e-08	18
immature T cell	2.95e-08	18
mature T cell	2.95e-08	18
immature alpha-beta T cell	2.95e-08	18
T cell	1.26e-07	25
pro-T cell	1.26e-07	25

Uber Anatomy

Ontology term	p-value	n
adult organism	6.66e-47	114
neural tube	6.56e-30	56
neural rod	6.56e-30	56
future spinal cord	6.56e-30	56
neural keel	6.56e-30	56
regional part of nervous system	4.46e-28	53
regional part of brain	4.46e-28	53
central nervous system	2.20e-25	81
nervous system	2.99e-25	89
brain	6.75e-25	68
future brain	6.75e-25	68
regional part of forebrain	1.46e-23	41
forebrain	1.46e-23	41
anterior neural tube	1.46e-23	41
future forebrain	1.46e-23	41
neurectoderm	9.36e-21	86
neural plate	8.22e-20	82
presumptive neural plate	8.22e-20	82
telencephalon	4.03e-19	34
brain grey matter	4.41e-19	34
gray matter	4.41e-19	34
regional part of telencephalon	7.73e-18	32
cerebral hemisphere	9.35e-18	32
pre-chordal neural plate	4.27e-15	61
regional part of cerebral cortex	4.10e-14	22
cerebral cortex	1.90e-13	25
pallium	1.90e-13	25
neocortex	6.31e-13	20
ectoderm-derived structure	1.30e-12	171
ectoderm	1.30e-12	171
presumptive ectoderm	1.30e-12	171
ecto-epithelium	1.51e-12	104
organ system subdivision	6.47e-09	223
structure with developmental contribution from neural crest	2.44e-08	132
posterior neural tube	1.49e-07	15
chordal neural plate	1.49e-07	15
neural nucleus	3.41e-07	9
nucleus of brain	3.41e-07	9
basal ganglion	4.06e-07	9
nuclear complex of neuraxis	4.06e-07	9
aggregate regional part of brain	4.06e-07	9
collection of basal ganglia	4.06e-07	9
cerebral subcortex	4.06e-07	9

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	0.321379
MA0004.1	0.558729
MA0006.1	1.01439
MA0007.1	0.539222
MA0009.1	1.03681
MA0014.1	0.262822
MA0017.1	0.432438
MA0019.1	0.7124
MA0024.1	0.929647
MA0025.1	1.17262
MA0027.1	2.65688
MA0028.1	1.05129
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	1.45353
MA0050.1	0.545671
MA0051.1	0.661179
MA0052.1	0.959373
MA0055.1	0.213007
MA0056.1	0
MA0057.1	0.450439
MA0058.1	1.16137
MA0059.1	1.15845
MA0060.1	0.737586
MA0061.1	0.23892
MA0063.1	0
MA0066.1	0.66601
MA0067.1	1.35893
MA0068.1	0.578694
MA0069.1	1.02175
MA0070.1	1.01032
MA0071.1	0.625297
MA0072.1	1.00572
MA0073.1	0.00563817
MA0074.1	0.660398
MA0076.1	1.19721
MA0077.1	0.997832
MA0078.1	0.763954
MA0081.1	1.15882
MA0083.1	1.04447
MA0084.1	1.5477
MA0087.1	1.00322
MA0088.1	2.86388
MA0089.1	0
MA0090.1	0.490736
MA0091.1	0.561458
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	0.314898
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	1.84113
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	0.811435
MA0145.1	0.107156
MA0146.1	1.05598
MA0147.1	0.87383
MA0148.1	0.584698
MA0149.1	2.52795
MA0062.2	1.22729
MA0035.2	0.621793
MA0039.2	0.200862
MA0138.2	0.765223
MA0002.2	0.255126
MA0137.2	1.87543
MA0104.2	1.35181
MA0047.2	0.695777
MA0112.2	0.332548
MA0065.2	0.109623
MA0150.1	0.484557
MA0151.1	0
MA0152.1	0.629368
MA0153.1	1.13732
MA0154.1	0.132326
MA0155.1	0.318517
MA0156.1	0.417278
MA0157.1	0.810597
MA0158.1	0
MA0159.1	0.328286
MA0160.1	0.600559
MA0161.1	0
MA0162.1	0.62636
MA0163.1	0.273773
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	0.289793
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
ATF3#467	3	11.2315872630044	0.00159345997118423	0.0100403840682057
E2F1#1869	6	4.90738921487932	7.15746523583771e-05	0.00112679908315595
ELF1#1997	6	4.25809795880754	0.000167722477628883	0.00205210494858047
ELK4#2005	3	8.11784082923401	0.00405611313418576	0.0194079076199765
FOXA1#3169	3	5.54070987469273	0.0119217877786028	0.0433787267466641
GABPB1#2553	5	5.88973653015181	0.000300017597367021	0.00309834251472504
HEY1#23462	6	4.04011104310571	0.000229896855580751	0.00253085250342553
MAX#4149	4	4.30170367267141	0.00664492391067637	0.028296061661385
NFKB1#4790	5	4.5733861868282	0.0010219625937113	0.00724397660680155
NRF1#4899	4	8.14018629847394	0.000589217554838338	0.00493482696148846
PAX5#5079	4	4.44637702078522	0.00587473351924079	0.0263609578524592
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380106168045537
POU2F2#5452	4	6.07074937182835	0.00181532620952452	0.0108935218338618
SIX5#147912	5	14.2389294628825	3.91539088341565e-06	0.000127508421725303
SREBF2#6721	1	72.8238770685579	0.0136536157528913	0.0481697792661626
SRF#6722	4	9.1981188414452	0.000367240458248586	0.00365766032987069
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.0057290468852957
TBP#6908	6	3.70677068709639	0.00038541647290796	0.00377674151004264
TCF7L2#6934	3	5.38508828156867	0.0129048877993104	0.046404544032233
YY1#7528	5	4.09264229154488	0.00174336546284953	0.0107248245022408
ZBTB33#10009	2	10.5549083433271	0.0137425073714059	0.0483853193325779
ZNF143#7702	5	11.2507304601899	1.25426047727876e-05	0.000309239164274119
ZNF263#10127	4	5.48122775800712	0.00267560938060723	0.0147445107693773

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.