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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000119,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001007,UBERON:0001041,UBERON:0001062,UBERON:0001173,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002100,UBERON:0002110,UBERON:0002294,UBERON:0002323,UBERON:0002417,UBERON:0002423,UBERON:0002532,UBERON:0002553,UBERON:0003104,UBERON:0003914,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004458,UBERON:0004912,UBERON:0004921,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0005911,UBERON:0007026,UBERON:0009142
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000119,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001007,UBERON:0001041,UBERON:0001062,UBERON:0001173,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002100,UBERON:0002110,UBERON:0002294,UBERON:0002323,UBERON:0002417,UBERON:0002423,UBERON:0002532,UBERON:0002553,UBERON:0003104,UBERON:0003914,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004458,UBERON:0004912,UBERON:0004921,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0005911,UBERON:0007026,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:0101120
|fonse_cell_line=FF:0101120
|fonse_cell_line_closure=FF:0101120
|fonse_cell_line_closure=FF:0101120

Revision as of 16:41, 29 March 2012


Name:gall bladder carcinoma cell line:TGBC14TKB
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuegall bladder
dev stageNA
sexfemale
ageunknown
cell typeunclassifiable
cell lineTGBC14TKB
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-penis0.0699
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-lymphoma0.529
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11256

Jaspar motifP-value
MA0002.21.75861e-5
MA0003.10.941
MA0004.10.821
MA0006.10.341
MA0007.10.554
MA0009.10.736
MA0014.10.155
MA0017.10.519
MA0018.20.44
MA0019.10.929
MA0024.12.10024e-6
MA0025.10.998
MA0027.10.441
MA0028.10.00222
MA0029.10.895
MA0030.10.127
MA0031.10.501
MA0035.20.97
MA0038.10.0135
MA0039.27.42152e-4
MA0040.10.00823
MA0041.10.183
MA0042.10.19
MA0043.10.336
MA0046.10.23
MA0047.20.547
MA0048.10.856
MA0050.19.0097e-7
MA0051.14.78796e-5
MA0052.10.221
MA0055.10.00463
MA0057.10.941
MA0058.10.552
MA0059.10.154
MA0060.17.00746e-10
MA0061.18.93618e-4
MA0062.20.00509
MA0065.20.42
MA0066.10.258
MA0067.10.143
MA0068.10.0522
MA0069.10.408
MA0070.10.24
MA0071.10.699
MA0072.10.695
MA0073.10.77
MA0074.10.806
MA0076.10.00228
MA0077.10.65
MA0078.10.444
MA0079.20.88
MA0080.21.02071e-6
MA0081.10.0105
MA0083.10.117
MA0084.10.036
MA0087.10.373
MA0088.10.547
MA0090.10.0416
MA0091.10.00187
MA0092.10.232
MA0093.10.845
MA0099.29.2937e-7
MA0100.10.922
MA0101.10.0557
MA0102.20.815
MA0103.14.53539e-6
MA0104.20.684
MA0105.16.74548e-6
MA0106.10.837
MA0107.10.0229
MA0108.20.317
MA0111.10.75
MA0112.20.102
MA0113.10.199
MA0114.10.288
MA0115.10.0932
MA0116.10.0115
MA0117.10.16
MA0119.10.578
MA0122.10.691
MA0124.10.943
MA0125.10.0326
MA0131.10.825
MA0135.10.0242
MA0136.11.09066e-4
MA0137.20.171
MA0138.20.00166
MA0139.10.401
MA0140.10.362
MA0141.10.131
MA0142.10.348
MA0143.10.0801
MA0144.10.88
MA0145.10.746
MA0146.10.0604
MA0147.10.508
MA0148.10.279
MA0149.10.41
MA0150.10.00375
MA0152.10.173
MA0153.10.0358
MA0154.10.00784
MA0155.10.593
MA0156.10.0832
MA0157.10.151
MA0159.10.677
MA0160.10.695
MA0162.10.352
MA0163.10.195
MA0164.10.265
MA0258.10.216
MA0259.10.895



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: CNhs11256

Novel motifP-value
10.419
100.677
1000.43
1010.785
1020.796
1030.062
1040.61
1050.738
1060.0467
1070.183
1080.711
1090.451
110.0928
1100.811
1110.264
1120.219
1130.28
1140.0219
1150.999
1160.561
1170.412
1180.85
1190.429
120.343
1200.33
1210.366
1220.807
1230.193
1240.114
1250.573
1260.755
1270.369
1280.0127
1290.998
130.0715
1300.613
1310.313
1320.474
1330.00822
1340.334
1350.00902
1360.0255
1370.216
1380.0625
1390.0117
140.754
1400.735
1410.822
1420.995
1430.00352
1440.193
1450.48
1460.552
1470.884
1480.078
1490.144
150.25
1500.402
1510.297
1520.915
1530.111
1540.671
1550.182
1560.612
1570.93
1580.712
1590.133
160.593
1600.242
1610.418
1620.369
1630.607
1640.957
1650.567
1660.663
1670.653
1680.589
1690.966
170.72
180.032
190.142
20.608
200.349
210.903
220.724
230.0611
240.599
250.831
260.662
270.644
280.836
290.711
30.292
300.711
310.185
320.0182
330.256
340.402
350.0409
360.941
370.327
380.851
390.601
40.866
400.325
410.00856
420.553
430.159
440.948
450.81
460.107
470.938
480.946
490.0967
50.33
500.381
510.544
520.915
530.544
540.597
550.999
560.664
570.796
580.464
590.113
60.458
600.292
610.594
620.105
630.643
640.549
650.0558
660.221
670.35
680.129
690.47
70.579
700.264
710.522
720.826
730.983
740.0374
750.935
760.644
770.655
780.659
790.133
80.0874
800.0343
810.0748
820.00109
830.594
840.589
850.00516
860.403
870.508
880.716
890.0741
90.187
900.0593
910.24
920.16
930.409
940.257
950.826
960.151
970.65
980.0575
990.621



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: CNhs11256


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)

UBERON: Anatomy
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000119 (cell layer)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001007 (digestive system)
0001041 (foregut)
0001062 (anatomical entity)
0001173 (biliary tree)
0001555 (digestive tract)
0002050 (embryonic structure)
0002075 (viscus)
0002100 (trunk)
0002110 (gallbladder)
0002294 (biliary system)
0002323 (body cavity)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003914 (epithelial tube)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004458 (body cavity or lining)
0004912 (biliary bud)
0004921 (subdivision of digestive tract)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0007026 (primitive gut)
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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