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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=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100787
|fonse_cell_line=FF:0100787
|fonse_cell_line_closure=FF:0100787
|fonse_cell_line_closure=FF:0100787

Revision as of 16:43, 29 March 2012


Name:gastric cancer cell line:AZ521
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
sexunknown
ageunknown
cell typeunclassifiable
cell lineAZ521
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-penis0.0183
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-lymphoma0.509
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11286

Jaspar motifP-value
MA0002.26.17494e-4
MA0003.10.078
MA0004.10.509
MA0006.10.419
MA0007.10.445
MA0009.10.85
MA0014.10.876
MA0017.10.0331
MA0018.20.255
MA0019.10.419
MA0024.18.91852e-4
MA0025.10.817
MA0027.10.393
MA0028.11.8742e-4
MA0029.10.471
MA0030.10.244
MA0031.10.891
MA0035.20.144
MA0038.14.34681e-4
MA0039.20.716
MA0040.10.315
MA0041.10.272
MA0042.10.274
MA0043.10.0904
MA0046.10.189
MA0047.20.338
MA0048.10.163
MA0050.12.40829e-4
MA0051.10.00226
MA0052.10.021
MA0055.10.018
MA0057.10.213
MA0058.10.263
MA0059.10.836
MA0060.15.36005e-11
MA0061.10.0276
MA0062.21.17326e-4
MA0065.20.149
MA0066.10.374
MA0067.10.95
MA0068.10.123
MA0069.10.556
MA0070.10.00791
MA0071.10.754
MA0072.10.38
MA0073.10.808
MA0074.10.286
MA0076.14.56708e-5
MA0077.10.663
MA0078.10.969
MA0079.20.758
MA0080.21.35621e-9
MA0081.10.0795
MA0083.10.0215
MA0084.10.361
MA0087.10.241
MA0088.10.203
MA0090.10.713
MA0091.10.0276
MA0092.10.0778
MA0093.10.319
MA0099.28.41154e-13
MA0100.10.103
MA0101.10.455
MA0102.20.0114
MA0103.10.743
MA0104.20.25
MA0105.10.00616
MA0106.10.776
MA0107.10.184
MA0108.20.0087
MA0111.10.877
MA0112.23.23401e-5
MA0113.10.0287
MA0114.10.672
MA0115.10.912
MA0116.10.0367
MA0117.10.801
MA0119.10.114
MA0122.10.919
MA0124.10.146
MA0125.10.235
MA0131.10.0738
MA0135.10.204
MA0136.19.5186e-6
MA0137.20.173
MA0138.20.0176
MA0139.10.563
MA0140.10.0772
MA0141.10.274
MA0142.10.932
MA0143.10.207
MA0144.10.0382
MA0145.10.0728
MA0146.10.199
MA0147.10.293
MA0148.10.624
MA0149.10.893
MA0150.10.00929
MA0152.10.738
MA0153.10.668
MA0154.10.00781
MA0155.10.133
MA0156.10.44
MA0157.10.861
MA0159.10.306
MA0160.10.353
MA0162.10.0829
MA0163.10.009
MA0164.10.834
MA0258.10.00483
MA0259.10.37



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: CNhs11286

Novel motifP-value
10.471
100.414
1000.377
1010.762
1020.76
1030.378
1040.481
1050.865
1061.396e-4
1070.0206
1080.649
1090.538
110.29
1100.714
1110.35
1120.0251
1130.137
1140.111
1150.588
1160.809
1170.718
1180.757
1190.146
120.715
1200.597
1210.839
1220.905
1230.894
1240.678
1250.745
1260.541
1270.161
1280.00104
1290.991
130.598
1300.038
1310.0186
1320.876
1330.519
1340.521
1350.00527
1360.246
1370.349
1380.0368
1390.0164
140.704
1400.552
1410.503
1420.75
1430.0659
1440.586
1450.312
1460.669
1470.38
1480.152
1490.0593
150.299
1500.503
1510.0906
1520.134
1530.296
1540.753
1550.961
1560.415
1570.872
1580.662
1590.462
160.312
1600.165
1610.853
1620.693
1630.297
1640.352
1650.167
1661
1670.507
1680.839
1690.00831
170.29
180.208
190.112
20.0924
200.126
210.874
220.154
230.00779
240.786
250.598
260.402
270.0445
280.788
290.886
30.219
300.228
310.662
320.0156
330.708
340.485
350.68
360.9
370.143
380.534
390.367
40.213
400.814
410.348
420.774
430.148
440.158
450.399
460.112
470.8
480.729
490.356
50.242
500.902
510.489
520.0619
530.281
540.467
550.227
560.284
570.848
580.249
590.0404
60.992
600.0171
610.881
620.12
630.312
640.422
650.087
660.0295
670.382
680.13
690.734
70.786
700.165
710.234
720.219
730.309
740.745
750.892
760.585
770.0933
780.977
790.0465
80.392
800.45
810.288
820.0175
830.344
840.657
850.0113
860.616
870.822
880.528
890.0591
90.0581
900.484
910.0242
920.16
930.802
940.171
950.607
960.37
970.784
980.194
990.781



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: CNhs11286


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

DOID: Disease
0050686 (organ system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
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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