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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 infection, 24hr
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-penis0
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 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: CNhs11047

Jaspar motifP-value
MA0002.20.0395
MA0003.10.173
MA0004.10.322
MA0006.10.877
MA0007.10.827
MA0009.10.64
MA0014.10.914
MA0017.10.0582
MA0018.20.00113
MA0019.10.253
MA0024.10.0035
MA0025.10.4
MA0027.10.568
MA0028.12.22641e-5
MA0029.10.00662
MA0030.10.992
MA0031.10.0494
MA0035.28.11438e-4
MA0038.10.0375
MA0039.20.137
MA0040.10.735
MA0041.10.465
MA0042.10.835
MA0043.10.0408
MA0046.10.688
MA0047.20.716
MA0048.10.383
MA0050.10.692
MA0051.10.0394
MA0052.10.812
MA0055.10.187
MA0057.10.295
MA0058.10.234
MA0059.10.481
MA0060.11.18898e-32
MA0061.10.852
MA0062.21.37747e-7
MA0065.20.114
MA0066.10.07
MA0067.10.274
MA0068.10.379
MA0069.10.84
MA0070.10.127
MA0071.10.499
MA0072.10.0119
MA0073.10.982
MA0074.10.507
MA0076.17.91304e-7
MA0077.10.919
MA0078.10.473
MA0079.20.0519
MA0080.20.0286
MA0081.10.862
MA0083.10.0184
MA0084.10.603
MA0087.10.553
MA0088.10.289
MA0090.10.242
MA0091.10.213
MA0092.10.162
MA0093.10.234
MA0099.20.644
MA0100.10.57
MA0101.10.167
MA0102.20.522
MA0103.10.574
MA0104.20.119
MA0105.10.0169
MA0106.10.431
MA0107.10.0959
MA0108.20.137
MA0111.10.36
MA0112.25.99671e-6
MA0113.10.253
MA0114.10.213
MA0115.10.84
MA0116.10.00239
MA0117.10.512
MA0119.10.0289
MA0122.10.702
MA0124.10.86
MA0125.10.647
MA0131.10.403
MA0135.10.393
MA0136.10.749
MA0137.20.69
MA0138.20.103
MA0139.10.954
MA0140.12.26295e-8
MA0141.10.151
MA0142.10.433
MA0143.10.303
MA0144.10.4
MA0145.10.3
MA0146.10.201
MA0147.10.198
MA0148.10.471
MA0149.10.927
MA0150.10.31
MA0152.10.56
MA0153.10.619
MA0154.10.0037
MA0155.10.17
MA0156.10.133
MA0157.10.00386
MA0159.10.264
MA0160.10.369
MA0162.10.179
MA0163.10.02
MA0164.10.699
MA0258.10.00144
MA0259.10.283



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: CNhs11047

Novel motifP-value
10.266
100.608
1000.55
1010.576
1020.633
1030.67
1040.834
1050.648
1060.00621
1070.0503
1080.718
1090.682
110.159
1100.247
1110.701
1121.40966e-4
1130.447
1140.0889
1150.961
1160.346
1170.915
1180.0526
1190.435
120.743
1200.638
1210.75
1220.505
1230.294
1240.019
1250.916
1260.975
1270.681
1280.0844
1290.678
130.778
1308.41019e-4
1310.654
1320.671
1330.841
1340.572
1350.232
1360.113
1370.353
1380.195
1390.358
140.215
1400.576
1410.688
1420.833
1430.102
1440.529
1450.46
1460.735
1470.35
1480.464
1490.313
150.27
1500.831
1510.093
1520.392
1530.815
1540.327
1550.734
1560.754
1570.977
1580.477
1590.656
160.226
1600.112
1610.875
1620.886
1630.76
1643.82654e-7
1650.6
1660.529
1670.599
1680.506
1699.81638e-4
170.19
180.437
190.0825
20.105
200.195
210.53
220.143
230.00638
240.868
250.887
260.387
270.038
280.745
290.999
30.0878
300.555
310.594
320.0697
330.76
340.238
350.513
360.595
370.685
380.334
390.938
40.00121
400.996
410.72
420.553
430.447
440.421
450.545
460.0925
470.308
480.24
490.467
50.695
500.647
510.376
520.25
530.473
540.323
550.533
560.603
570.188
580.428
590.393
60.72
600.0933
610.967
620.149
630.085
640.275
650.127
661.78811e-12
670.835
680.876
690.913
70.694
700.51
710.281
720.396
730.452
740.558
750.843
760.951
770.051
780.912
790.529
80.073
800.339
810.314
820.144
830.384
840.649
850.0323
860.601
870.157
880.52
890.05
90.109
900.397
910.00791
920.203
930.663
940.0684
950.843
960.236
970.595
980.398
990.497



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: CNhs11047


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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