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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120
|fonse_cell_line=FF:0101120
|fonse_cell_line_closure=FF:0101120
|fonse_cell_line_closure=FF:0101120

Revision as of 16:33, 29 March 2012


Name:giant cell carcinoma cell line:Lu99B
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stage63 year old adult
sexmale
age63
cell typeunclassifiable
cell lineLu99B
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-0.0542
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-lymphoma0.0509
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs10751

Jaspar motifP-value
MA0002.20.0805
MA0003.10.0532
MA0004.10.236
MA0006.10.618
MA0007.10.431
MA0009.10.826
MA0014.10.674
MA0017.10.61
MA0018.20.289
MA0019.10.232
MA0024.10.549
MA0025.10.9
MA0027.10.562
MA0028.15.92746e-5
MA0029.10.854
MA0030.10.143
MA0031.10.193
MA0035.20.585
MA0038.10.401
MA0039.20.014
MA0040.10.496
MA0041.10.654
MA0042.10.986
MA0043.10.168
MA0046.10.873
MA0047.20.878
MA0048.10.0102
MA0050.13.57849e-5
MA0051.10.195
MA0052.10.162
MA0055.10.00185
MA0057.10.792
MA0058.10.325
MA0059.10.815
MA0060.10.16
MA0061.10.276
MA0062.21.65609e-4
MA0065.20.941
MA0066.10.502
MA0067.10.766
MA0068.10.747
MA0069.10.942
MA0070.10.0364
MA0071.10.78
MA0072.10.521
MA0073.10.859
MA0074.10.301
MA0076.18.60947e-4
MA0077.10.769
MA0078.10.856
MA0079.20.421
MA0080.20.00702
MA0081.10.779
MA0083.10.0699
MA0084.10.319
MA0087.10.401
MA0088.10.262
MA0090.10.0888
MA0091.10.042
MA0092.10.174
MA0093.10.163
MA0099.29.55393e-13
MA0100.10.61
MA0101.10.911
MA0102.20.505
MA0103.10.194
MA0104.20.583
MA0105.10.00386
MA0106.10.119
MA0107.10.991
MA0108.20.429
MA0111.10.39
MA0112.20.0288
MA0113.10.104
MA0114.10.372
MA0115.10.708
MA0116.10.0381
MA0117.10.452
MA0119.10.837
MA0122.10.166
MA0124.10.818
MA0125.10.745
MA0131.10.75
MA0135.10.87
MA0136.10.834
MA0137.20.126
MA0138.20.695
MA0139.10.73
MA0140.10.716
MA0141.10.373
MA0142.10.00625
MA0143.10.779
MA0144.10.585
MA0145.10.577
MA0146.10.16
MA0147.10.695
MA0148.10.892
MA0149.10.128
MA0150.11.54037e-4
MA0152.10.382
MA0153.10.86
MA0154.10.0336
MA0155.10.775
MA0156.10.068
MA0157.10.799
MA0159.10.986
MA0160.10.536
MA0162.10.153
MA0163.10.00829
MA0164.10.415
MA0258.10.0686
MA0259.10.672



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: CNhs10751

Novel motifP-value
10.743
100.994
1000.661
1010.835
1020.63
1030.0869
1040.683
1050.803
1060.481
1070.575
1080.952
1090.804
110.275
1100.773
1110.623
1120.128
1130.106
1140.357
1150.136
1160.181
1170.129
1180.285
1190.54
120.756
1200.48
1210.777
1220.673
1230.43
1240.743
1250.232
1260.433
1270.321
1280.0346
1290.837
130.356
1300.455
1310.415
1320.742
1330.0458
1340.471
1350.00324
1360.201
1370.614
1380.935
1390.621
140.986
1400.0705
1410.631
1420.00707
1430.118
1440.357
1450.792
1460.324
1470.465
1480.107
1490.0387
150.933
1500.481
1510.402
1520.424
1530.833
1540.391
1550.418
1560.919
1570.354
1580.503
1590.918
160.165
1600.771
1610.686
1620.556
1630.741
1640.367
1650.768
1660.75
1670.245
1680.497
1690.714
170.942
180.218
190.0839
20.199
200.0167
210.398
220.958
230.15
240.388
250.0703
260.0645
270.0115
280.356
290.986
30.945
300.807
310.344
321.4571e-5
330.163
340.518
350.234
360.708
370.53
380.927
390.957
40.624
400.461
410.0662
420.692
430.0432
440.399
450.845
460.11
470.975
480.734
490.348
50.174
500.048
510.901
520.572
530.646
540.6
550.843
560.758
570.436
580.128
590.00998
60.742
600.22
610.0941
620.0114
630.496
640.118
650.128
660.407
670.28
680.158
690.723
70.226
700.959
710.121
720.757
730.685
740.84
750.524
760.269
770.738
780.975
790.0481
80.412
800.491
810.045
820.178
830.656
840.374
850.0017
860.291
870.139
880.502
890.548
90.175
900.663
910.0187
920.785
930.295
940.107
950.362
960.236
970.665
980.517
990.249



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: CNhs10751


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
4 (disease)

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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