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{{f5samples
{{f5samples
|F5samples=
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|ancestors_in_anatomy_facet=UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000160,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001045,UBERON:0001048,UBERON:0001062,UBERON:0001264,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002100,UBERON:0002108,UBERON:0002114,UBERON:0002323,UBERON:0002532,UBERON:0002553,UBERON:0003104,UBERON:0003921,UBERON:0003922,UBERON:0003923,UBERON:0003924,UBERON:0003928,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004458,UBERON:0004921,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0007026,UBERON:0007329,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 16:40, 29 March 2012


Name:ductal cell carcinoma cell line:KLM-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepancreas
dev stageNA
sexunknown
ageNA
cell typeduct cell
cell lineKLM-1
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-0.00203
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-lymphoma0.436
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: CNhs11100

Jaspar motifP-value
MA0002.20.00126
MA0003.10.868
MA0004.10.33
MA0006.10.584
MA0007.10.18
MA0009.10.128
MA0014.10.0134
MA0017.10.678
MA0018.28.65936e-4
MA0019.10.746
MA0024.10.012
MA0025.10.0664
MA0027.10.917
MA0028.15.99776e-5
MA0029.10.0421
MA0030.10.0748
MA0031.10.0146
MA0035.20.0579
MA0038.10.00795
MA0039.22.0821e-4
MA0040.10.362
MA0041.10.904
MA0042.10.65
MA0043.16.68776e-4
MA0046.10.757
MA0047.20.00184
MA0048.10.933
MA0050.10.35
MA0051.10.303
MA0052.10.44
MA0055.10.0107
MA0057.10.502
MA0058.10.553
MA0059.10.982
MA0060.14.18085e-7
MA0061.10.00115
MA0062.25.08337e-6
MA0065.20.377
MA0066.10.0723
MA0067.10.864
MA0068.10.858
MA0069.10.858
MA0070.10.473
MA0071.10.256
MA0072.10.908
MA0073.10.884
MA0074.10.866
MA0076.11.14742e-5
MA0077.10.0802
MA0078.10.384
MA0079.20.199
MA0080.20.00245
MA0081.10.0673
MA0083.10.884
MA0084.10.183
MA0087.10.803
MA0088.10.449
MA0090.10.022
MA0091.11.64925e-4
MA0092.10.409
MA0093.10.35
MA0099.25.54627e-5
MA0100.10.255
MA0101.10.0169
MA0102.20.863
MA0103.11.04751e-7
MA0104.20.185
MA0105.11.6475e-6
MA0106.10.00533
MA0107.10.00253
MA0108.20.0833
MA0111.10.413
MA0112.20.137
MA0113.10.0423
MA0114.10.481
MA0115.10.191
MA0116.10.0232
MA0117.10.987
MA0119.10.981
MA0122.10.797
MA0124.10.887
MA0125.10.0297
MA0131.10.349
MA0135.10.486
MA0136.10.629
MA0137.20.603
MA0138.20.132
MA0139.10.117
MA0140.10.174
MA0141.10.245
MA0142.10.0376
MA0143.10.812
MA0144.10.505
MA0145.10.196
MA0146.10.994
MA0147.10.111
MA0148.10.00498
MA0149.10.0843
MA0150.10.304
MA0152.10.461
MA0153.10.632
MA0154.10.0326
MA0155.10.278
MA0156.10.288
MA0157.10.264
MA0159.10.159
MA0160.10.885
MA0162.10.543
MA0163.10.00206
MA0164.10.609
MA0258.10.0875
MA0259.10.227



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: CNhs11100

Novel motifP-value
10.984
100.692
1000.388
1010.96
1020.261
1030.431
1040.52
1050.366
1060.0507
1070.341
1080.976
1090.21
110.146
1100.504
1110.314
1120.104
1130.116
1140.0603
1150.313
1160.0685
1170.892
1180.613
1190.523
120.898
1200.252
1210.903
1220.254
1230.578
1240.928
1250.597
1260.807
1270.649
1280.0139
1290.386
130.105
1300.443
1310.145
1320.769
1330.0176
1340.15
1350.0831
1360.0228
1370.255
1380.708
1390.0566
140.895
1400.497
1410.429
1420.988
1430.00951
1440.119
1450.183
1460.701
1470.559
1480.571
1490.112
150.905
1500.435
1510.723
1520.288
1530.948
1540.443
1550.759
1560.636
1570.958
1580.855
1590.86
160.887
1600.352
1610.997
1620.771
1630.713
1640.315
1650.974
1660.0872
1670.495
1680.8
1690.833
170.464
180.313
190.0665
20.814
200.592
210.353
220.468
230.133
240.515
250.306
260.582
270.578
280.297
290.538
30.219
300.247
310.0747
321.14782e-4
330.247
340.435
350.0758
360.967
370.216
380.969
390.634
40.418
400.546
410.145
420.978
430.0475
440.131
450.804
460.369
470.763
480.978
490.107
50.497
500.264
510.381
520.94
530.918
540.527
550.751
560.968
570.589
580.712
590.302
60.579
600.833
610.719
620.531
630.613
640.655
650.191
660.0087
670.923
680.0129
690.92
70.171
700.185
710.6
720.449
730.172
740.0145
750.778
760.837
770.661
780.473
798.96015e-4
80.26
800.569
810.029
820.00574
830.612
840.676
850.0151
860.391
870.0659
880.464
890.334
90.249
900.556
910.19
920.109
930.845
940.0698
950.973
960.154
970.193
980.329
990.812



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: CNhs11100


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
0050686 (organ system cancer)
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
170 (endocrine gland cancer)
1793 (pancreatic cancer)
305 (carcinoma)
3498 (pancreatic ductal adenocarcinoma)
4 (disease)
4074 (pancreas adenocarcinoma)
4905 (pancreatic carcinoma)

UBERON: Anatomy
0000058 (duct)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000160 (intestine)
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)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001045 (midgut)
0001048 (primordium)
0001062 (anatomical entity)
0001264 (pancreas)
0001555 (digestive tract)
0002050 (embryonic structure)
0002075 (viscus)
0002100 (trunk)
0002108 (small intestine)
0002114 (duodenum)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003921 (pancreas primordium)
0003922 (pancreatic epithelial bud)
0003923 (dorsal pancreatic bud)
0003928 (digestive system duct)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004458 (body cavity or lining)
0004921 (subdivision of digestive tract)
0005177 (trunk region element)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)
0007329 (pancreatic duct)
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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