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Revision as of 18:13, 27 November 2014


Name:Wilms' tumor cell line:G-401
Species:Human (Homo sapiens)
Library ID:CNhs11892
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuekidney
dev stageNA
sexmale
age3 months
cell typeunclassifiable
cell lineG-401
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00006011
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11892 CAGE DRX007794 DRR008666
Accession ID Hg19

Library idBAMCTSS
CNhs11892 DRZ000091 DRZ001476
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.215
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11892

Jaspar motifP-value
MA0002.25.21649e-5
MA0003.10.134
MA0004.10.063
MA0006.10.7
MA0007.10.339
MA0009.10.0434
MA0014.10.659
MA0017.10.777
MA0018.20.239
MA0019.10.676
MA0024.12.52761e-5
MA0025.10.206
MA0027.10.732
MA0028.10.0617
MA0029.10.239
MA0030.10.196
MA0031.10.307
MA0035.20.389
MA0038.10.00579
MA0039.20.262
MA0040.10.0904
MA0041.10.205
MA0042.10.16
MA0043.10.616
MA0046.10.479
MA0047.20.355
MA0048.10.00745
MA0050.16.60702e-14
MA0051.14.07582e-8
MA0052.10.386
MA0055.15.41895e-4
MA0057.10.437
MA0058.10.0719
MA0059.10.222
MA0060.14.38202e-16
MA0061.10.00388
MA0062.20.995
MA0065.20.381
MA0066.10.947
MA0067.10.285
MA0068.10.903
MA0069.10.897
MA0070.10.3
MA0071.10.688
MA0072.10.648
MA0073.10.55
MA0074.10.843
MA0076.10.0806
MA0077.10.996
MA0078.10.322
MA0079.20.447
MA0080.21.29106e-11
MA0081.10.112
MA0083.10.548
MA0084.10.552
MA0087.10.146
MA0088.10.00911
MA0090.10.604
MA0091.10.145
MA0092.10.157
MA0093.10.0448
MA0099.22.1617e-11
MA0100.10.115
MA0101.10.178
MA0102.25.02012e-4
MA0103.10.855
MA0104.20.0515
MA0105.10.00924
MA0106.10.157
MA0107.10.00392
MA0108.20.287
MA0111.10.372
MA0112.20.00312
MA0113.10.00968
MA0114.10.27
MA0115.10.0478
MA0116.10.0203
MA0117.10.622
MA0119.10.202
MA0122.10.614
MA0124.10.028
MA0125.10.108
MA0131.10.603
MA0135.10.924
MA0136.17.2833e-9
MA0137.20.00816
MA0138.20.983
MA0139.10.656
MA0140.10.303
MA0141.10.97
MA0142.10.159
MA0143.10.354
MA0144.12.18879e-4
MA0145.10.281
MA0146.10.358
MA0147.10.0571
MA0148.10.538
MA0149.10.996
MA0150.10.00148
MA0152.10.629
MA0153.10.387
MA0154.10.0289
MA0155.10.234
MA0156.12.40635e-5
MA0157.10.0825
MA0159.10.992
MA0160.10.977
MA0162.10.997
MA0163.10.129
MA0164.10.918
MA0258.10.196
MA0259.10.238



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11892

Novel motifP-value
10.857
100.166
1000.161
1010.929
1020.0723
1030.37
1040.21
1050.646
1060.0081
1070.0947
1080.636
1090.76
110.863
1100.929
1110.43
1120.202
1130.0443
1140.0512
1150.684
1160.8
1170.306
1180.683
1190.0793
120.55
1200.546
1210.355
1220.507
1230.743
1240.301
1250.652
1260.342
1270.82
1280.102
1290.792
130.0542
1300.0419
1310.257
1320.722
1330.316
1340.247
1350.0384
1360.787
1370.954
1380.208
1390.0134
140.641
1400.0511
1410.423
1420.68
1430.167
1440.46
1450.745
1460.194
1470.723
1480.0122
1490.078
150.213
1500.721
1510.0677
1520.54
1530.0748
1540.163
1550.539
1560.316
1570.946
1580.167
1590.531
160.613
1600.277
1610.434
1620.301
1630.297
1640.28
1650.0938
1660.631
1670.686
1680.0389
1690.249
170.624
180.181
190.262
20.2
200.431
210.698
220.433
232.69268e-4
240.86
250.437
260.377
270.0865
280.905
290.968
30.409
300.656
310.774
320.0319
330.536
340.543
350.836
360.549
370.953
380.438
390.503
40.671
400.383
410.1
420.768
430.126
440.717
450.428
460.339
470.567
480.859
490.373
50.0641
500.907
510.735
520.409
530.103
540.585
550.257
560.811
570.816
580.0312
590.15
60.998
600.0554
610.9
620.0225
630.284
640.531
650.103
660.0089
670.637
680.059
690.419
70.969
700.054
710.319
720.26
730.5
740.336
750.298
760.891
770.829
780.703
790.18
80.674
800.00378
810.488
820.159
830.467
840.727
850.0631
860.456
870.0926
880.926
890.303
90.131
900.386
910.067
920.0069
930.122
940.0753
950.0275
960.426
970.339
980.43
990.89



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs11892


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

DOID: Disease
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002113 (kidney)
0002100 (trunk)
0000062 (organ)
0000475 (organism subdivision)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0009569 (subdivision of trunk)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0005172 (abdomen element)
0005173 (abdominal segment element)
0011143 (upper urinary tract)
0001008 (renal system)
0002417 (abdominal segment of trunk)
0000916 (abdomen)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100067 (kidney cell line sample)
0103192 (renal cancer cell line sample)
0102586 (G-401 cell sample)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
UBERON:0003104 (mesenchyme)
UBERON:0003918 (kidney mesenchyme)
UBERON:0007687 (kidney field)

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