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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000945,UBERON:0001007,UBERON:0001041,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0003104,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005409,UBERON:0005423,UBERON:0007026,UBERON:0009142
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000945,UBERON:0001007,UBERON:0001041,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0003104,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005409,UBERON:0005423,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:0100787,FF:0101120
|fonse_cell_line=FF:0100787,FF:0101120
|fonse_cell_line_closure=FF:0100787,FF:0101120
|fonse_cell_line_closure=FF:0100787,FF:0101120

Revision as of 16:54, 29 March 2012


Name:gastric adenocarcinoma cell line:MKN45
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuestomach
dev stageNA
sexfemale
age62
cell typeunclassifiable
cell lineMKN45
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-penis0.198
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-lymphoma0.152
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: CNhs11819

Jaspar motifP-value
MA0002.20.00694
MA0003.10.795
MA0004.10.172
MA0006.10.945
MA0007.10.556
MA0009.10.054
MA0014.10.155
MA0017.10.0182
MA0018.20.124
MA0019.10.266
MA0024.10.0288
MA0025.10.738
MA0027.10.871
MA0028.10.00483
MA0029.10.484
MA0030.10.111
MA0031.10.399
MA0035.20.0311
MA0038.10.613
MA0039.20.0179
MA0040.10.0619
MA0041.10.716
MA0042.10.884
MA0043.10.805
MA0046.15.09572e-44
MA0047.23.94618e-4
MA0048.10.406
MA0050.12.50539e-4
MA0051.10.0762
MA0052.10.00946
MA0055.17.0056e-4
MA0057.10.251
MA0058.10.547
MA0059.10.0721
MA0060.11.1736e-4
MA0061.11.88946e-4
MA0062.20.00596
MA0065.20.00379
MA0066.10.0272
MA0067.10.143
MA0068.10.0485
MA0069.10.621
MA0070.10.418
MA0071.10.749
MA0072.10.744
MA0073.10.606
MA0074.10.772
MA0076.10.00811
MA0077.10.958
MA0078.10.437
MA0079.20.361
MA0080.24.78075e-7
MA0081.10.00373
MA0083.14.15842e-4
MA0084.10.0488
MA0087.10.163
MA0088.10.324
MA0090.10.04
MA0091.10.0233
MA0092.10.0351
MA0093.10.24
MA0099.24.29242e-4
MA0100.10.532
MA0101.10.00894
MA0102.20.529
MA0103.13.66933e-9
MA0104.20.00347
MA0105.12.5936e-5
MA0106.10.0409
MA0107.19.13758e-4
MA0108.24.64345e-4
MA0111.10.805
MA0112.20.0995
MA0113.10.208
MA0114.11.56083e-5
MA0115.10.118
MA0116.10.0471
MA0117.10.159
MA0119.10.257
MA0122.10.32
MA0124.10.619
MA0125.10.46
MA0131.10.518
MA0135.10.432
MA0136.14.36734e-5
MA0137.20.216
MA0138.20.268
MA0139.10.0224
MA0140.10.771
MA0141.10.743
MA0142.10.499
MA0143.10.319
MA0144.10.112
MA0145.10.407
MA0146.10.688
MA0147.10.0031
MA0148.16.83192e-5
MA0149.10.0593
MA0150.10.0111
MA0152.10.28
MA0153.11.95592e-26
MA0154.10.0198
MA0155.10.239
MA0156.10.0243
MA0157.10.999
MA0159.10.585
MA0160.10.496
MA0162.10.834
MA0163.10.627
MA0164.10.0457
MA0258.10.287
MA0259.10.115



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: CNhs11819

Novel motifP-value
10.868
100.499
1000.473
1010.443
1020.775
1030.544
1040.887
1050.565
1060.912
1070.976
1080.435
1090.54
110.434
1100.289
1110.838
1120.124
1130.012
1140.79
1150.53
1160.263
1170.748
1180.836
1190.743
120.599
1200.484
1210.475
1220.084
1230.963
1240.84
1250.107
1260.3
1270.434
1280.674
1290.4
130.00522
1300.0608
1310.158
1320.349
1330.00651
1340.598
1350.0557
1360.062
1370.407
1380.319
1390.0501
140.919
1400.717
1410.294
1420.754
1430.0452
1440.334
1450.413
1460.747
1470.891
1480.633
1490.531
150.944
1500.831
1510.927
1520.568
1530.996
1540.743
1550.767
1560.665
1570.222
1580.506
1590.545
160.663
1600.58
1610.978
1620.649
1630.801
1640.599
1650.448
1660.643
1670.775
1680.682
1690.521
170.735
180.193
190.0587
20.375
200.238
210.649
220.478
230.0592
240.456
250.828
260.106
270.856
280.784
290.482
30.305
300.84
310.544
320.0312
330.593
340.585
350.53
360.424
370.648
380.995
390.658
40.431
400.532
410.00767
420.934
430.16
440.795
450.978
460.931
470.785
480.853
490.299
50.269
500.416
510.472
520.54
530.386
540.393
550.621
560.881
570.903
580.777
590.304
60.575
600.742
610.263
620.226
630.522
640.827
650.429
660.0397
670.514
680.0536
690.513
70.464
700.487
710.662
720.402
730.419
740.184
750.359
760.498
770.367
780.321
790.348
80.896
800.239
810.209
820.0767
830.595
840.778
850.0766
860.49
870.214
880.869
890.145
90.054
900.666
910.0843
920.491
930.771
940.0762
950.199
960.0568
970.85
980.763
990.59



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: CNhs11819


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)
299 (adenocarcinoma)
305 (carcinoma)
3119 (gastrointestinal system cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000945 (stomach)
0001007 (digestive system)
0001041 (foregut)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
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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