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Revision as of 17:39, 27 November 2014


Name:gastric adenocarcinoma cell line:MKN1
Species:Human (Homo sapiens)
Library ID:CNhs11737
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuestomach
dev stageNA
sexmale
age72
cell typeunclassifiable
cell lineMKN1
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005958
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11737 CAGE DRX007890 DRR008762
Accession ID Hg19

Library idBAMCTSS
CNhs11737 DRZ000187 DRZ001572
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-penis0.126
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-lymphoma0.259
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
C115-pituitary-Neural-caudate-putamen-amygdala-medulla-hippocampus0
C116-myeloma-xeroderma-tonsil-CD19-spleen-lymph-trachea0
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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: CNhs11737

Jaspar motifP-value
MA0002.20.0628
MA0003.10.809
MA0004.10.0569
MA0006.10.82
MA0007.10.889
MA0009.10.462
MA0014.10.153
MA0017.10.551
MA0018.20.0874
MA0019.10.129
MA0024.10.321
MA0025.10.495
MA0027.10.618
MA0028.16.64954e-7
MA0029.10.948
MA0030.10.987
MA0031.10.992
MA0035.20.272
MA0038.10.0794
MA0039.20.00691
MA0040.10.135
MA0041.10.823
MA0042.10.623
MA0043.10.00354
MA0046.10.222
MA0047.20.506
MA0048.10.775
MA0050.10.103
MA0051.10.00454
MA0052.10.132
MA0055.10.0842
MA0057.10.161
MA0058.10.19
MA0059.10.0956
MA0060.10.116
MA0061.17.19524e-4
MA0062.23.71779e-4
MA0065.20.63
MA0066.10.447
MA0067.10.0216
MA0068.10.0083
MA0069.10.931
MA0070.10.864
MA0071.10.592
MA0072.10.593
MA0073.10.936
MA0074.10.766
MA0076.12.88232e-7
MA0077.10.335
MA0078.10.857
MA0079.20.195
MA0080.21.49539e-10
MA0081.10.0155
MA0083.10.00646
MA0084.10.27
MA0087.10.204
MA0088.10.562
MA0090.10.104
MA0091.10.0645
MA0092.10.293
MA0093.10.0569
MA0099.25.25805e-7
MA0100.10.355
MA0101.10.00345
MA0102.20.0115
MA0103.14.99416e-5
MA0104.20.124
MA0105.10.015
MA0106.10.39
MA0107.17.514e-5
MA0108.20.00785
MA0111.10.456
MA0112.20.452
MA0113.10.251
MA0114.10.43
MA0115.10.375
MA0116.10.0288
MA0117.10.0198
MA0119.10.564
MA0122.10.608
MA0124.10.0397
MA0125.10.0906
MA0131.10.531
MA0135.10.321
MA0136.15.45252e-7
MA0137.20.565
MA0138.20.424
MA0139.10.0457
MA0140.10.74
MA0141.10.921
MA0142.10.311
MA0143.10.704
MA0144.10.346
MA0145.10.305
MA0146.10.0318
MA0147.10.00777
MA0148.10.994
MA0149.10.358
MA0150.10.0124
MA0152.10.989
MA0153.10.973
MA0154.10.00655
MA0155.10.898
MA0156.10.00335
MA0157.10.576
MA0159.10.0121
MA0160.10.999
MA0162.10.953
MA0163.10.282
MA0164.10.374
MA0258.10.939
MA0259.10.00523



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: CNhs11737

Novel motifP-value
10.968
100.74
1000.186
1010.134
1020.52
1030.555
1040.883
1050.59
1060.586
1070.175
1080.272
1090.0464
110.274
1100.437
1110.315
1120.351
1139.21012e-5
1140.358
1150.114
1160.627
1170.398
1180.289
1190.509
120.118
1200.358
1210.937
1220.783
1230.0173
1240.0534
1250.11
1260.302
1270.49
1280.0124
1290.266
130.227
1300.533
1310.0243
1320.326
1330.255
1340.143
1350.0619
1360.00684
1370.00738
1380.432
1390.828
140.127
1400.533
1410.639
1420.562
1430.422
1440.922
1450.142
1460.418
1470.992
1480.478
1490.561
150.52
1500.441
1510.635
1520.0368
1530.0506
1540.31
1550.219
1560.754
1570.854
1580.333
1590.123
160.72
1600.597
1610.372
1620.577
1630.807
1640.732
1650.837
1660.432
1670.519
1680.961
1690.156
170.934
180.984
190.406
20.471
200.486
210.343
220.976
230.18
240.595
250.951
260.331
270.521
280.718
290.0171
30.406
300.944
310.276
320.201
330.235
340.207
350.133
360.146
370.0469
380.888
390.675
40.523
400.885
410.015
420.359
430.458
440.0549
450.87
460.545
470.979
480.877
490.303
50.253
500.977
510.847
520.169
530.0879
540.604
550.0873
560.973
570.7
580.493
590.467
60.425
600.523
610.347
620.634
630.772
640.809
650.989
660.34
670.953
680.534
690.235
70.69
700.648
710.506
720.364
730.00622
740.271
750.0782
760.0936
770.743
780.654
790.981
80.541
800.113
810.219
820.722
830.453
840.112
850.442
860.078
870.811
880.947
890.247
90.233
900.124
910.184
920.0862
930.53
940.138
950.4
960.424
970.742
980.399
990.394



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: CNhs11737


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)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0002178 (epithelial cell of stomach)

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)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000945 (stomach)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
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)
0010039 (food storage organ)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001041 (foregut)

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)
0100787 (gastric cancer cell line sample)
0102380 (gastric adenocarcinoma cell line sample)
0102384 (MKN-1 cell 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
CL:0000223 (endodermal cell)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)

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