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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000468,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001062,UBERON:0002050,UBERON:0002346,UBERON:0002532,UBERON:0005423
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000468,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001062,UBERON:0002050,UBERON:0002346,UBERON:0002532,UBERON:0005423
|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:10663-109C6
|fonse_cell_line=FF:10663-109C6
|fonse_cell_line_closure=FF:10663-109C6
|fonse_cell_line_closure=FF:10663-109C6

Revision as of 16:51, 29 March 2012


Name:neuroectodermal tumor cell line:FU-RPNT-2
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
age10
cell typeunclassifiable
cell lineFU-RPNT-2
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-penis0.352
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-lymphoma0.348
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0.374
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 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: CNhs11753

Jaspar motifP-value
MA0002.21.36324e-6
MA0003.10.0372
MA0004.10.373
MA0006.10.159
MA0007.10.227
MA0009.10.939
MA0014.10.773
MA0017.10.00322
MA0018.20.15
MA0019.10.0125
MA0024.10.00162
MA0025.10.272
MA0027.10.3
MA0028.10.29
MA0029.10.498
MA0030.10.311
MA0031.10.259
MA0035.20.0961
MA0038.10.796
MA0039.20.235
MA0040.10.226
MA0041.10.31
MA0042.10.434
MA0043.10.695
MA0046.10.0948
MA0047.20.3
MA0048.10.0673
MA0050.10.0206
MA0051.10.014
MA0052.10.0887
MA0055.10.0936
MA0057.10.178
MA0058.10.372
MA0059.10.547
MA0060.10.171
MA0061.10.0213
MA0062.20.746
MA0065.20.0148
MA0066.10.142
MA0067.10.499
MA0068.16.67307e-5
MA0069.10.803
MA0070.10.879
MA0071.10.615
MA0072.10.696
MA0073.10.0523
MA0074.10.595
MA0076.10.145
MA0077.10.64
MA0078.10.573
MA0079.20.244
MA0080.26.49467e-9
MA0081.10.0407
MA0083.10.261
MA0084.10.074
MA0087.10.262
MA0088.10.117
MA0090.10.222
MA0091.10.362
MA0092.10.398
MA0093.10.411
MA0099.22.03547e-12
MA0100.10.812
MA0101.10.0179
MA0102.20.123
MA0103.10.358
MA0104.20.0704
MA0105.10.522
MA0106.10.748
MA0107.10.00784
MA0108.20.549
MA0111.10.693
MA0112.24.46488e-4
MA0113.10.443
MA0114.10.0159
MA0115.10.196
MA0116.10.453
MA0117.10.937
MA0119.10.218
MA0122.10.374
MA0124.10.387
MA0125.10.6
MA0131.10.178
MA0135.10.0356
MA0136.12.23025e-7
MA0137.20.264
MA0138.20.693
MA0139.10.887
MA0140.10.0719
MA0141.10.0801
MA0142.10.518
MA0143.10.445
MA0144.10.0137
MA0145.10.00105
MA0146.10.544
MA0147.10.0628
MA0148.10.841
MA0149.10.00254
MA0150.10.00402
MA0152.10.953
MA0153.10.047
MA0154.10.0897
MA0155.10.271
MA0156.19.74304e-4
MA0157.10.153
MA0159.10.0899
MA0160.10.0285
MA0162.10.234
MA0163.10.412
MA0164.10.61
MA0258.10.222
MA0259.10.128



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: CNhs11753

Novel motifP-value
10.718
100.98
1000.418
1010.606
1020.814
1030.0021
1040.686
1050.36
1060.0356
1070.0759
1080.7
1090.125
110.673
1100.697
1110.912
1120.648
1130.997
1140.068
1150.304
1160.508
1170.953
1180.591
1190.732
120.55
1200.391
1210.353
1220.121
1234.31211e-5
1240.499
1250.813
1260.119
1270.127
1280.436
1290.456
130.289
1300.938
1310.706
1320.379
1330.717
1340.931
1350.0866
1360.208
1370.21
1380.521
1390.764
140.688
1400.874
1410.863
1420.535
1430.00229
1440.481
1450.878
1460.965
1470.574
1480.0674
1490.124
150.455
1500.364
1510.365
1520.00809
1530.391
1540.165
1550.618
1560.491
1570.82
1580.267
1590.298
160.26
1600.901
1610.259
1620.547
1630.794
1640.479
1650.546
1660.701
1670.542
1680.62
1690.0101
170.268
180.168
190.139
20.0808
200.257
210.138
220.0578
230.0101
240.192
250.467
260.813
270.112
280.632
290.845
30.746
300.0893
310.221
320.0653
330.788
340.11
350.982
360.348
370.309
380.465
390.833
40.554
400.755
410.0552
420.58
430.338
440.307
450.152
460.451
470.872
480.915
490.951
50.454
500.845
510.775
520.308
530.148
540.517
550.623
560.752
570.349
580.563
590.0257
60.0783
600.114
610.325
620.205
630.96
640.776
650.286
660.574
670.918
680.714
690.478
70.869
700.35
710.612
720.323
730.0488
740.0854
750.873
760.197
770.132
780.718
790.545
80.706
800.0437
810.844
820.826
830.727
840.281
850.133
860.722
870.453
880.442
890.0195
90.032
900.274
910.671
920.373
930.406
940.587
950.378
960.747
970.822
980.567
990.705



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: CNhs11753


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
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
171 (neuroectodermal tumor)
2994 (germ cell cancer)
3095 (germ cell and embryonal cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0005423 (developing anatomical structure)

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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