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{{f5samples
{{f5samples
|F5samples=
|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_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,FF:0100669
|fonse_cell_line=FF:0100067,FF:0100669
|fonse_cell_line_closure=FF:0100067,FF:0100669
|fonse_cell_line_closure=FF:0100067,FF:0100669

Revision as of 16:37, 29 March 2012


Name:embryonic kidney cell line: HEK293/SLAM untreated
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
sexNA
ageNA
cell typeunclassifiable
cell lineHEK293/SLAM
companyNA
collaborationChieko Kai (University of Tokyo)
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-0.0124
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-lymphoma0.608
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs11046

Jaspar motifP-value
MA0002.28.80609e-4
MA0003.10.142
MA0004.10.511
MA0006.10.528
MA0007.10.547
MA0009.10.723
MA0014.10.519
MA0017.10.0289
MA0018.20.0948
MA0019.10.198
MA0024.19.30818e-7
MA0025.10.287
MA0027.10.683
MA0028.18.57692e-5
MA0029.10.0783
MA0030.10.663
MA0031.10.762
MA0035.20.0436
MA0038.10.00286
MA0039.20.429
MA0040.10.206
MA0041.10.471
MA0042.10.348
MA0043.10.0376
MA0046.10.759
MA0047.20.511
MA0048.10.367
MA0050.11.98326e-9
MA0051.12.79814e-4
MA0052.10.0272
MA0055.10.0739
MA0057.10.353
MA0058.10.357
MA0059.10.478
MA0060.12.08438e-26
MA0061.10.00829
MA0062.21.24569e-5
MA0065.20.0822
MA0066.10.119
MA0067.10.56
MA0068.10.0293
MA0069.10.44
MA0070.10.0242
MA0071.10.842
MA0072.10.0644
MA0073.10.54
MA0074.10.515
MA0076.11.92399e-6
MA0077.10.563
MA0078.10.297
MA0079.20.557
MA0080.21.89772e-9
MA0081.10.229
MA0083.10.0178
MA0084.10.211
MA0087.10.745
MA0088.10.0406
MA0090.10.0122
MA0091.10.00597
MA0092.10.0771
MA0093.10.357
MA0099.22.11164e-7
MA0100.10.307
MA0101.10.203
MA0102.20.00368
MA0103.10.576
MA0104.20.108
MA0105.10.00136
MA0106.10.701
MA0107.10.0378
MA0108.20.25
MA0111.10.625
MA0112.23.09033e-5
MA0113.10.159
MA0114.10.313
MA0115.10.645
MA0116.10.0127
MA0117.10.789
MA0119.10.112
MA0122.10.496
MA0124.10.53
MA0125.10.107
MA0131.10.282
MA0135.10.716
MA0136.10.00361
MA0137.20.801
MA0138.20.064
MA0139.10.819
MA0140.10.0616
MA0141.10.293
MA0142.10.464
MA0143.10.284
MA0144.10.0308
MA0145.10.0688
MA0146.10.128
MA0147.10.19
MA0148.10.32
MA0149.10.726
MA0150.10.00344
MA0152.10.393
MA0153.10.604
MA0154.10.0141
MA0155.10.124
MA0156.10.591
MA0157.10.917
MA0159.10.0496
MA0160.10.321
MA0162.10.159
MA0163.10.0125
MA0164.10.873
MA0258.10.00224
MA0259.10.268



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: CNhs11046

Novel motifP-value
10.22
100.528
1000.41
1010.717
1020.818
1030.167
1040.688
1050.406
1062.11687e-4
1070.0294
1080.653
1090.211
110.156
1100.383
1110.747
1120.0173
1130.17
1140.0202
1150.972
1160.674
1170.567
1180.482
1190.0995
120.852
1200.953
1210.918
1220.506
1230.285
1240.478
1250.7
1260.56
1270.239
1280.0213
1290.611
130.854
1300.0541
1310.263
1320.52
1330.267
1340.628
1356.3029e-4
1360.159
1370.157
1380.237
1390.0415
140.577
1400.293
1410.529
1420.769
1430.339
1440.409
1450.344
1460.851
1470.191
1480.25
1490.0165
150.275
1500.472
1510.186
1520.0222
1530.379
1540.556
1550.957
1560.816
1570.444
1580.445
1590.637
160.291
1600.467
1610.779
1620.769
1630.313
1640.104
1650.787
1660.49
1670.322
1680.0605
1690.00668
170.107
180.0956
190.0769
20.171
200.381
210.456
220.102
230.00131
240.94
250.873
260.415
270.0789
280.981
290.648
30.175
300.523
310.544
320.00603
330.874
340.268
350.522
360.875
370.151
380.349
390.523
40.157
400.83
410.391
420.741
430.127
440.451
450.403
460.1
470.512
480.457
490.373
50.278
500.645
510.23
520.143
530.403
540.231
550.0637
560.659
570.362
580.274
590.077
60.89
600.0194
610.838
620.0936
630.173
640.601
650.0345
668.32558e-4
670.77
680.726
690.696
70.797
700.00719
710.302
720.198
730.081
740.811
750.417
760.854
770.142
780.823
790.0694
80.37
800.0528
810.414
820.0127
830.118
840.702
850.00188
860.442
870.469
880.56
890.0783
90.077
900.485
910.0399
920.0246
930.501
940.012
950.511
960.083
971
980.237
990.73



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: CNhs11046


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

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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