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Coexpression cluster:C4118

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Full id: C4118_thyroid_clear_kidney_anaplastic_Renal_serous_endometrioid



Phase1 CAGE Peaks

Hg19::chr2:113984760..113984792,+p@chr2:113984760..113984792
+
Hg19::chr2:113999199..113999214,+p@chr2:113999199..113999214
+
Hg19::chr2:114036488..114036504,-p1@PAX8


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
kidney2.14e-3426
kidney mesenchyme2.14e-3426
upper urinary tract2.14e-3426
kidney rudiment2.14e-3426
kidney field2.14e-3426
nephron tubule epithelium1.05e-3010
cavitated compound organ3.35e-2831
excretory tube2.07e-2716
kidney epithelium2.07e-2716
nephron epithelium2.02e-2415
renal tubule2.02e-2415
nephron tubule2.02e-2415
nephron2.02e-2415
uriniferous tubule2.02e-2415
nephrogenic mesenchyme2.02e-2415
urinary system structure1.59e-1947
renal system4.95e-1948
reproductive organ3.52e-1848
female reproductive organ1.49e-1637
female reproductive system1.49e-1637
cortex of kidney2.56e-1512
renal parenchyma2.56e-1512
female organism1.26e-1441
abdomen element1.61e-1454
abdominal segment element1.61e-1454
reproductive structure4.86e-1459
reproductive system4.86e-1459
thyroid gland2.28e-135
pharyngeal pouch2.28e-135
thyroid diverticulum2.28e-135
pharyngeal pouch 22.28e-135
thyroid primordium2.28e-135
internal genitalia5.12e-1325
abdominal segment of trunk1.09e-1260
abdomen1.09e-1260
renal cortex tubule1.50e-123
region of nephron tubule1.50e-123
proximal tubule1.50e-123
cortex4.83e-1215
parenchyma4.83e-1215
compound organ9.34e-1168
mesonephros1.63e-109
pronephros1.63e-109
nephrogenic cord1.63e-109
pronephric mesoderm1.63e-109
rostral part of nephrogenic cord1.63e-109
presumptive pronephric mesoderm1.63e-109
uterus3.43e-1021
gonad5.94e-1021
indifferent external genitalia5.94e-1021
indifferent gonad5.94e-1021
gonad primordium5.94e-1021
female gonad9.44e-1013
embryonic uterus1.14e-0922
internal female genitalia1.14e-0922
external genitalia1.92e-0922
abdomen connective tissue3.38e-092
abdominal segment connective tissue3.38e-092
trunk connective tissue3.38e-092
interstitial tissue3.38e-092
extraglomerular mesangium3.38e-092
kidney interstitium3.38e-092
juxtaglomerular apparatus3.38e-092
mesangium3.38e-092
urogenital ridge1.53e-0811
mesonephric epithelium6.10e-088
mesonephric tubule6.10e-088
nephric duct6.10e-088
renal duct6.10e-088
mesonephric duct6.10e-088
pronephric duct6.10e-088
intraembryonic coelom8.39e-0812
body cavity precursor2.01e-0754


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.990225
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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


No analysis results for this cluster

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.