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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000118,UBERON:0000119,UBERON:0000170,UBERON:0000171,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002048,UBERON:0002050,UBERON:0002224,UBERON:0002532,UBERON:0003104,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005597,UBERON:0005911,UBERON:0007026,UBERON:0008947,UBERON:0009142
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000118,UBERON:0000119,UBERON:0000170,UBERON:0000171,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002048,UBERON:0002050,UBERON:0002224,UBERON:0002532,UBERON:0003104,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005597,UBERON:0005911,UBERON:0007026,UBERON:0008947,UBERON:0009142
|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:0100353,FF:0101120
|fonse_cell_line=FF:0100353,FF:0101120
|fonse_cell_line_closure=FF:0100353,FF:0101120
|fonse_cell_line_closure=FF:0100353,FF:0101120

Revision as of 16:54, 29 March 2012


Name:small cell lung carcinoma cell line:WA-hT
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 stageNA
sexmale
age56
cell typeunclassifiable
cell lineWA-hT
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-penis0.334
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-lymphoma0.441
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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-teratocarcinoma0.162
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0.932
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: CNhs11812

Jaspar motifP-value
MA0002.29.86675e-6
MA0003.10.416
MA0004.10.15
MA0006.10.586
MA0007.10.49
MA0009.10.626
MA0014.10.692
MA0017.10.0171
MA0018.20.00215
MA0019.10.816
MA0024.19.9188e-5
MA0025.10.00823
MA0027.10.902
MA0028.10.194
MA0029.10.413
MA0030.10.00918
MA0031.10.0442
MA0035.20.958
MA0038.12.10758e-4
MA0039.20.156
MA0040.10.654
MA0041.10.23
MA0042.10.166
MA0043.10.0126
MA0046.10.651
MA0047.20.0123
MA0048.10.156
MA0050.10.00788
MA0051.10.00313
MA0052.10.678
MA0055.10.617
MA0057.10.459
MA0058.10.127
MA0059.10.824
MA0060.14.4212e-20
MA0061.10.00742
MA0062.20.0322
MA0065.20.0104
MA0066.10.0312
MA0067.10.757
MA0068.10.191
MA0069.10.862
MA0070.10.0324
MA0071.10.265
MA0072.10.454
MA0073.10.712
MA0074.10.132
MA0076.10.0224
MA0077.10.0476
MA0078.10.784
MA0079.20.271
MA0080.20.00513
MA0081.10.0944
MA0083.10.108
MA0084.10.743
MA0087.10.573
MA0088.10.285
MA0090.10.00219
MA0091.10.0485
MA0092.10.0593
MA0093.10.0984
MA0099.21.4302e-8
MA0100.10.23
MA0101.10.0329
MA0102.20.4
MA0103.16.15433e-4
MA0104.20.35
MA0105.12.31496e-5
MA0106.10.141
MA0107.10.0195
MA0108.20.0328
MA0111.10.464
MA0112.25.81755e-5
MA0113.10.0485
MA0114.10.0581
MA0115.10.477
MA0116.11.78299e-4
MA0117.10.666
MA0119.10.0584
MA0122.10.332
MA0124.10.774
MA0125.10.0338
MA0131.10.346
MA0135.10.915
MA0136.10.843
MA0137.20.0843
MA0138.20.957
MA0139.10.301
MA0140.10.345
MA0141.10.042
MA0142.10.224
MA0143.10.156
MA0144.10.286
MA0145.10.229
MA0146.10.32
MA0147.10.729
MA0148.10.0102
MA0149.10.126
MA0150.18.58789e-4
MA0152.10.933
MA0153.10.0925
MA0154.16.0733e-4
MA0155.10.528
MA0156.10.44
MA0157.10.248
MA0159.10.364
MA0160.10.164
MA0162.10.196
MA0163.14.60268e-8
MA0164.10.35
MA0258.10.00361
MA0259.10.543



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: CNhs11812

Novel motifP-value
10.143
100.13
1000.834
1010.492
1020.254
1030.0342
1040.343
1050.498
1060.00445
1070.0592
1080.632
1090.14
110.0873
1100.23
1110.0138
1120.0919
1130.408
1147.46577e-4
1150.912
1160.163
1170.122
1180.178
1190.164
120.508
1200.24
1210.6
1220.329
1230.243
1240.859
1250.853
1260.452
1270.356
1280.0478
1290.569
130.261
1300.73
1310.795
1320.997
1330.373
1340.979
1350.00607
1360.324
1370.0222
1380.845
1390.122
140.813
1400.0165
1410.77
1420.687
1430.376
1440.0287
1450.121
1460.321
1470.721
1480.024
1490.0747
150.113
1500.46
1510.383
1520.0781
1530.374
1540.88
1550.798
1560.272
1570.676
1580.763
1590.0372
160.133
1600.0783
1610.329
1620.776
1630.854
1640.0458
1650.0679
1660.332
1670.652
1680.0871
1690.0137
170.25
180.28
190.182
20.76
200.945
210.166
220.174
230.02
240.141
250.719
260.0583
270.877
280.93
290.289
30.0302
300.865
310.494
327.34074e-4
330.701
340.483
350.126
360.0758
370.0571
380.379
390.0684
40.627
400.407
410.164
420.122
430.0903
440.493
450.552
460.0644
470.243
480.156
490.138
50.232
500.455
510.219
520.154
530.567
540.233
550.0474
560.564
570.286
580.146
590.0413
60.49
600.0461
610.685
620.0436
630.121
640.555
650.172
660.0945
670.543
680.94
690.874
70.462
700.0657
710.0678
720.434
730.0884
740.0484
750.184
760.651
770.0894
780.355
790.0324
80.0717
800.077
810.0897
820.0193
830.707
840.714
850.00313
860.176
870.872
880.427
890.0998
90.139
900.0365
910.162
920.0476
930.883
940.145
950.258
960.135
970.351
980.708
990.607



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: CNhs11812


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
0050615 (respiratory system cancer)
0050686 (organ system cancer)
0050687 (cell type cancer)
1324 (lung cancer)
1325 (bronchus cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
3904 (bronchogenic carcinoma)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000118 (lung bud)
0000119 (cell layer)
0000170 (pair of lungs)
0000171 (respiration organ)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002048 (lung)
0002050 (embryonic structure)
0002224 (thoracic cavity)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003258 (endoderm of foregut)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005423 (developing anatomical structure)
0005597 (lung primordium)
0005911 (endo-epithelium)
0007026 (primitive gut)
0008947 (respiratory primordium)
0009142 (entire embryonic mesenchyme)

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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