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{{f5samples
{{f5samples
|F5samples=
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|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0000489,UBERON:0000916,UBERON:0000922,UBERON:0001008,UBERON:0001062,UBERON:0002100,UBERON:0002113,UBERON:0002417,UBERON:0003103,UBERON:0005095,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005423,UBERON:0006554,UBERON:0007687
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100067
|fonse_cell_line=FF:0100067
|fonse_cell_line_closure=FF:0100067
|fonse_cell_line_closure=FF:0100067

Revision as of 16:49, 29 March 2012


Name:Wilms' tumor cell line:HFWT
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuekidney
dev stageNA
sexmale
age5 months
cell typeunclassifiable
cell lineHFWT
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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
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-penis-0.0543
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.0158
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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 no result for this sample


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: CNhs11728

Jaspar motifP-value
MA0002.20.0108
MA0003.10.0821
MA0004.10.797
MA0006.10.877
MA0007.10.823
MA0009.10.41
MA0014.10.844
MA0017.10.382
MA0018.20.954
MA0019.10.0249
MA0024.10.141
MA0025.10.935
MA0027.10.707
MA0028.10.0985
MA0029.10.0118
MA0030.10.986
MA0031.10.536
MA0035.20.578
MA0038.10.673
MA0039.20.959
MA0040.10.544
MA0041.10.733
MA0042.10.388
MA0043.10.0205
MA0046.10.677
MA0047.20.711
MA0048.10.693
MA0050.11.15051e-13
MA0051.12.20132e-9
MA0052.10.0639
MA0055.10.194
MA0057.10.726
MA0058.10.42
MA0059.10.28
MA0060.10.351
MA0061.16.3112e-4
MA0062.20.0046
MA0065.20.895
MA0066.10.747
MA0067.10.234
MA0068.10.169
MA0069.10.988
MA0070.10.364
MA0071.10.0722
MA0072.10.0546
MA0073.10.847
MA0074.10.637
MA0076.10.123
MA0077.10.0251
MA0078.10.00178
MA0079.20.683
MA0080.21.1061e-10
MA0081.10.0266
MA0083.10.00706
MA0084.10.117
MA0087.10.708
MA0088.10.835
MA0090.10.103
MA0091.10.86
MA0092.10.604
MA0093.10.836
MA0099.26.33402e-5
MA0100.10.447
MA0101.10.0193
MA0102.20.831
MA0103.10.56
MA0104.20.968
MA0105.13.47026e-5
MA0106.10.275
MA0107.10.00115
MA0108.21.20915e-4
MA0111.10.264
MA0112.20.0132
MA0113.10.623
MA0114.10.619
MA0115.10.0431
MA0116.10.00375
MA0117.10.23
MA0119.10.469
MA0122.10.445
MA0124.10.043
MA0125.10.471
MA0131.10.958
MA0135.10.264
MA0136.19.03026e-11
MA0137.20.0179
MA0138.20.773
MA0139.10.607
MA0140.10.728
MA0141.10.0402
MA0142.10.643
MA0143.10.984
MA0144.10.0082
MA0145.10.501
MA0146.10.152
MA0147.10.827
MA0148.10.973
MA0149.10.296
MA0150.10.0202
MA0152.10.568
MA0153.10.685
MA0154.10.0183
MA0155.10.741
MA0156.12.21577e-8
MA0157.10.0657
MA0159.10.221
MA0160.10.0315
MA0162.10.214
MA0163.15.50602e-6
MA0164.10.869
MA0258.10.447
MA0259.10.825



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: CNhs11728

Novel motifP-value
10.599
100.017
1000.445
1010.542
1020.632
1030.7
1040.507
1050.178
1060.0568
1070.798
1080.939
1090.24
110.177
1100.241
1110.449
1120.502
1130.379
1140.546
1150.183
1160.23
1170.146
1180.944
1190.766
120.257
1200.639
1210.356
1220.694
1230.0139
1240.512
1250.384
1260.628
1270.338
1280.998
1290.494
130.243
1300.987
1310.718
1320.837
1330.00403
1340.986
1350.242
1360.968
1370.225
1380.947
1390.132
140.525
1400.376
1410.803
1420.948
1430.71
1440.791
1450.656
1460.839
1470.605
1480.00266
1490.202
150.755
1500.335
1510.541
1520.161
1530.669
1540.751
1550.215
1560.374
1570.26
1580.36
1590.767
160.107
1600.0709
1610.376
1620.72
1630.389
1640.713
1650.854
1660.975
1670.675
1680.216
1690.0416
170.812
180.108
190.12
20.0997
200.622
210.705
220.274
230.292
240.209
250.0271
260.829
270.441
280.677
290.252
30.295
300.357
310.589
320.00504
330.334
340.892
350.158
360.143
370.0116
380.662
390.373
40.166
400.488
410.495
420.526
430.243
440.0829
450.897
460.94
470.379
480.285
490.72
50.809
500.93
510.597
520.257
530.837
540.503
550.16
560.773
570.0865
580.00551
590.0897
60.727
600.00458
610.911
620.00212
630.739
640.551
650.651
660.179
670.143
680.833
690.711
70.226
700.368
710.0138
720.301
730.0838
740.949
750.132
760.835
770.037
780.636
790.0145
80.739
800.537
810.852
820.305
830.94
840.721
850.127
860.617
870.637
880.747
890.0215
90.0407
900.556
910.699
920.419
930.687
940.891
950.202
960.523
970.922
980.0972
990.348



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: CNhs11728


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
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0000489 (cavitated compound organ)
0000916 (abdomen)
0000922 (embryo)
0001008 (renal system)
0001062 (anatomical entity)
0002100 (trunk)
0002113 (kidney)
0002417 (abdominal segment of trunk)
0003103 (compound organ)
0005095 (kidney rudiment)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005423 (developing anatomical structure)
0006554 (urinary system structure)
0007687 (kidney field)

FF: FANTOM5
NA

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
NA

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