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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:0000076,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,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 16:59, 29 March 2012


Name:anaplastic squamous cell carcinoma cell line:RPMI 2650
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuenasal septum
dev stageNA
sexmale
ageunknown
cell typeunclassifiable
cell lineRPMI 2650
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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-penis0.513
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-lymphoma0.526
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11889

Jaspar motifP-value
MA0002.28.9008e-5
MA0003.10.0234
MA0004.10.849
MA0006.10.495
MA0007.10.305
MA0009.10.991
MA0014.10.526
MA0017.10.0619
MA0018.20.19
MA0019.10.0995
MA0024.16.90328e-4
MA0025.10.357
MA0027.10.849
MA0028.10.3
MA0029.10.912
MA0030.10.649
MA0031.10.524
MA0035.20.264
MA0038.10.111
MA0039.20.31
MA0040.10.265
MA0041.10.323
MA0042.10.637
MA0043.10.7
MA0046.10.936
MA0047.20.362
MA0048.10.119
MA0050.10.00237
MA0051.10.023
MA0052.10.482
MA0055.10.00488
MA0057.10.418
MA0058.10.934
MA0059.10.753
MA0060.11.48527e-5
MA0061.10.00181
MA0062.20.996
MA0065.20.209
MA0066.10.15
MA0067.10.832
MA0068.10.309
MA0069.10.633
MA0070.10.604
MA0071.10.874
MA0072.10.779
MA0073.10.0787
MA0074.10.317
MA0076.10.203
MA0077.10.546
MA0078.10.636
MA0079.20.722
MA0080.26.15892e-10
MA0081.10.0521
MA0083.10.0218
MA0084.10.904
MA0087.10.624
MA0088.10.389
MA0090.10.566
MA0091.10.0254
MA0092.10.14
MA0093.10.804
MA0099.21.6981e-11
MA0100.10.332
MA0101.10.015
MA0102.20.0437
MA0103.10.621
MA0104.20.583
MA0105.14.0459e-4
MA0106.10.556
MA0107.10.00183
MA0108.20.307
MA0111.10.428
MA0112.23.6584e-5
MA0113.10.406
MA0114.10.344
MA0115.10.392
MA0116.10.0078
MA0117.10.649
MA0119.10.551
MA0122.10.525
MA0124.10.317
MA0125.10.187
MA0131.10.102
MA0135.10.0672
MA0136.14.99375e-9
MA0137.20.0341
MA0138.20.0564
MA0139.10.391
MA0140.10.389
MA0141.10.299
MA0142.10.799
MA0143.10.619
MA0144.10.00432
MA0145.10.0393
MA0146.10.803
MA0147.10.54
MA0148.10.646
MA0149.10.537
MA0150.14.94233e-4
MA0152.10.915
MA0153.10.366
MA0154.10.00264
MA0155.10.435
MA0156.11.57511e-5
MA0157.10.0961
MA0159.10.0651
MA0160.10.216
MA0162.10.268
MA0163.10.113
MA0164.10.939
MA0258.10.0404
MA0259.10.267



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: CNhs11889

Novel motifP-value
10.517
100.53
1000.454
1010.181
1020.583
1030.00451
1040.638
1050.933
1060.00118
1070.048
1080.464
1090.208
110.398
1100.821
1110.847
1120.283
1130.348
1140.063
1150.138
1160.793
1170.91
1180.624
1190.756
120.876
1200.273
1210.851
1220.34
1230.00212
1240.379
1250.94
1260.14
1270.0751
1280.146
1290.286
130.799
1300.481
1310.356
1320.883
1330.46
1340.415
1350.0576
1360.444
1370.572
1380.452
1390.774
140.861
1400.391
1410.799
1420.431
1434.71542e-4
1440.912
1450.89
1460.497
1470.482
1480.00396
1490.274
150.277
1500.416
1510.591
1520.0368
1530.935
1540.928
1550.406
1560.492
1570.466
1580.946
1590.47
160.236
1600.427
1610.7
1620.42
1630.149
1640.81
1650.233
1660.9
1670.238
1680.0526
1690.152
170.236
180.0526
190.105
20.199
200.173
210.894
220.125
230.00423
240.159
250.546
260.541
270.121
280.686
290.507
30.526
300.29
310.671
320.00921
330.385
340.304
350.662
360.577
370.16
380.673
390.323
40.726
400.851
410.0152
420.867
430.114
440.25
450.254
460.184
470.791
480.956
490.536
50.192
500.743
510.429
520.245
530.597
540.34
550.768
560.798
570.453
580.186
590.00433
60.362
600.0486
610.833
620.0399
630.358
640.595
650.152
660.469
670.695
680.849
690.988
70.643
700.321
710.137
720.204
730.137
740.0272
750.625
760.541
770.0752
780.542
790.0431
80.462
800.0598
810.629
820.151
830.313
840.341
850.0116
860.466
870.238
880.977
890.064
90.058
900.949
910.536
920.248
930.0965
940.385
950.514
960.579
970.778
980.657
990.626



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: CNhs11889


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)
0000076 (squamous epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
1749 (squamous cell carcinoma)
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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