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Coexpression cluster:C888: Difference between revisions

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}}
}}

Revision as of 19:32, 22 January 2013


Full id: C888_uterus_dura_CD14_mature_epididymis_prostate_cervix



Phase1 CAGE Peaks

Hg19::chr12:102791856..102791865,-p@chr12:102791856..102791865
-
Hg19::chr12:102872317..102872350,-p2@IGF1
Hg19::chr12:102874242..102874255,-p6@IGF1
Hg19::chr12:102874261..102874275,-p4@IGF1
Hg19::chr12:102874293..102874309,-p5@IGF1
Hg19::chr12:102874314..102874327,-p3@IGF1
Hg19::chr12:102874330..102874350,-p1@IGF1
Hg19::chr12:102874382..102874394,-p7@IGF1
Hg19::chr12:102874416..102874425,-p8@IGF1


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
fat cell8.43e-1515
Uber Anatomy
Ontology termp-valuen
adult organism7.82e-48114
regional part of cerebral cortex2.44e-1122
cerebral hemisphere9.13e-1132
telencephalon9.69e-1134
neural tube1.04e-1056
neural rod1.04e-1056
future spinal cord1.04e-1056
neural keel1.04e-1056
brain grey matter1.33e-1034
gray matter1.33e-1034
neocortex3.55e-1020
cavity lining8.80e-1012
serous membrane8.80e-1012
regional part of telencephalon9.48e-1032
regional part of forebrain1.79e-0941
forebrain1.79e-0941
anterior neural tube1.79e-0941
future forebrain1.79e-0941
cerebral cortex2.03e-0925
pallium2.03e-0925
regional part of nervous system3.08e-0953
regional part of brain3.08e-0953
organ system subdivision4.33e-09223
central nervous system4.06e-0881
nervous system5.64e-0889
neurectoderm8.57e-0886
neural plate2.77e-0782
presumptive neural plate2.77e-0782
omentum3.03e-076
peritoneum3.03e-076
abdominal cavity3.03e-076
visceral peritoneum3.03e-076
brain3.55e-0768
future brain3.55e-0768
structure with developmental contribution from neural crest7.26e-07132


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)
MA0003.10.000472949
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.00594475
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.11.10579
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.11.41801
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.11.02363
MA0056.10
MA0057.10.0725989
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.000336275
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.0408613
MA0089.10
MA0090.10.353576
MA0091.11.07263
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.13.17401
MA0122.10.934245
MA0124.12.42824
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.13.29243
MA0140.12.07572
MA0141.10.322254
MA0142.15.30972
MA0143.10.571113
MA0144.10.1885
MA0145.11.08897
MA0146.10.0045741
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.0006485
MA0138.20.608783
MA0002.20.905786
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.0433683
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.0402662
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.00648562
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.23.47892e-06
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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
CCNT2#90574.928156782082056.52167806614696e-050.00105878677996319
CEBPB#105176.199781486752641.39459740509258e-050.000336452664334637
CTCF#1066474.169088290169470.0001982812163300480.0023810845064153
GATA2#262479.91272468165315.71014888882728e-072.6329458710827e-05
NRF1#489979.496884014886267.65865712776971e-073.36500837933168e-05
POLR2A#543081.908847268051620.0116612289598830.0425775098357299
RAD21#588578.053915252021592.36147727378579e-068.37738875668866e-05
SRF#6722710.73113864835273.31352184322677e-071.65737982655537e-05
TAL1#6886723.23114630467571.59434073890572e-091.40279151163078e-07



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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