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|rna_box=106
|rna_box=106

Revision as of 19:07, 21 September 2012


Name:papillotubular adenocarcinoma cell line:TGBC18TKB
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueduodenum
dev stage79 year old adult
sexfemale
age79
cell typeunclassifiable
cell lineTGBC18TKB
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-0.0423
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-lymphoma0.312
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
C113-thyroid-throat-lung-lymph-small-colon-trachea0
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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



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: CNhs10734

Jaspar motifP-value
MA0002.20.493
MA0003.10.814
MA0004.10.997
MA0006.10.0739
MA0007.10.385
MA0009.10.176
MA0014.10.0741
MA0017.10.0505
MA0018.20.0647
MA0019.10.632
MA0024.10.0202
MA0025.10.0557
MA0027.10.821
MA0028.10.02
MA0029.10.523
MA0030.19.3441e-5
MA0031.10.00271
MA0035.20.0274
MA0038.10.133
MA0039.20.0015
MA0040.10.163
MA0041.10.952
MA0042.10.749
MA0043.10.0575
MA0046.13.65549e-4
MA0047.20.0017
MA0048.10.85
MA0050.18.54814e-4
MA0051.16.51867e-4
MA0052.10.459
MA0055.10.00528
MA0057.10.894
MA0058.10.991
MA0059.10.854
MA0060.10.0949
MA0061.10.314
MA0062.20.0163
MA0065.20.882
MA0066.10.921
MA0067.10.803
MA0068.10.22
MA0069.10.933
MA0070.10.55
MA0071.10.227
MA0072.10.511
MA0073.10.617
MA0074.10.985
MA0076.10.0715
MA0077.10.0952
MA0078.10.684
MA0079.20.156
MA0080.20.776
MA0081.10.0942
MA0083.10.815
MA0084.10.567
MA0087.10.533
MA0088.10.181
MA0090.10.0119
MA0091.10.00472
MA0092.10.124
MA0093.10.946
MA0099.21.13843e-9
MA0100.10.925
MA0101.10.0952
MA0102.20.33
MA0103.11.19672e-8
MA0104.20.464
MA0105.10.127
MA0106.10.494
MA0107.10.0606
MA0108.20.259
MA0111.10.706
MA0112.20.422
MA0113.10.24
MA0114.10.0811
MA0115.10.507
MA0116.10.0607
MA0117.10.389
MA0119.10.921
MA0122.10.27
MA0124.10.255
MA0125.10.0648
MA0131.10.973
MA0135.10.795
MA0136.10.797
MA0137.20.232
MA0138.20.00613
MA0139.10.831
MA0140.10.457
MA0141.10.263
MA0142.10.452
MA0143.10.393
MA0144.10.171
MA0145.10.0681
MA0146.10.0197
MA0147.10.619
MA0148.10.00386
MA0149.10.162
MA0150.10.529
MA0152.10.093
MA0153.13.07851e-4
MA0154.10.657
MA0155.10.486
MA0156.10.435
MA0157.10.33
MA0159.10.27
MA0160.10.654
MA0162.10.977
MA0163.10.00861
MA0164.10.928
MA0258.10.757
MA0259.10.373



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: CNhs10734

Novel motifP-value
10.434
100.908
1000.928
1010.0737
1020.56
1030.165
1040.875
1050.632
1060.368
1070.877
1080.788
1090.279
110.172
1100.758
1110.259
1120.308
1130.24
1140.119
1150.456
1160.154
1170.0207
1180.931
1190.65
120.564
1200.631
1210.289
1220.354
1230.855
1240.0194
1250.244
1260.834
1270.965
1280.105
1290.236
130.0816
1300.64
1310.0709
1320.394
1330.125
1340.499
1350.0183
1360.0881
1370.112
1380.0936
1390.205
140.878
1400.244
1410.042
1420.765
1430.0145
1440.11
1450.804
1460.361
1470.576
1480.831
1490.344
150.647
1500.245
1510.552
1520.0165
1530.311
1540.488
1550.913
1560.33
1570.429
1580.316
1590.246
160.83
1600.49
1610.302
1620.56
1630.922
1640.987
1650.892
1660.26
1670.627
1680.958
1690.135
170.443
180.0414
190.25
20.83
200.0896
210.794
220.738
230.705
240.918
250.748
260.737
270.485
280.5
290.858
30.534
300.151
310.219
324.06977e-5
330.0571
340.66
350.00335
360.972
370.642
380.529
390.865
40.563
400.423
410.0949
420.942
430.151
440.348
450.255
460.182
470.546
480.617
490.176
50.394
500.192
510.767
520.447
530.833
540.927
550.788
560.711
570.706
580.789
590.544
60.357
600.618
610.254
620.317
630.287
640.362
650.98
660.317
670.359
680.0365
690.294
70.646
700.911
710.371
720.752
730.0106
740.0323
750.389
760.842
770.425
780.0324
790.276
80.0909
800.601
810.00459
827.7262e-4
830.367
840.897
850.254
860.779
870.0677
880.684
890.442
90.554
900.186
910.104
920.337
930.847
940.036
950.0637
960.556
970.383
980.0574
990.76



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: CNhs10734


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)
0000548 (animal cell)
0000066 (epithelial cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
305 (carcinoma)
299 (adenocarcinoma)
3119 (gastrointestinal system cancer)
4929 (tubular adenocarcinoma)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002108 (small intestine)
0000160 (intestine)
0002394 (bile duct)
0004913 (hepatopancreatic ampulla)
0000058 (duct)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0004111 (anatomical conduit)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003703 (extrahepatic bile duct)
0003928 (digestive system duct)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0002114 (duodenum)
0005409 (gastrointestinal system)
0002294 (biliary system)
0001173 (biliary tree)
0002423 (hepatobiliary system)
0001174 (common bile duct)
0004914 (duodenal papilla)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0101120 (epithelial cell line sample)
0100167 (adenocarcinoma cell line sample)

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
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)

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