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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 16:33, 29 March 2012


Name:signet ring carcinoma cell line:Kato III
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
ageNA
cell typeunclassifiable
cell lineKato III
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-0.0402
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-lymphoma0.497
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: CNhs10753

Jaspar motifP-value
MA0002.20.409
MA0003.10.935
MA0004.10.00397
MA0006.10.477
MA0007.10.47
MA0009.10.0155
MA0014.10.05
MA0017.17.71166e-4
MA0018.20.356
MA0019.10.249
MA0024.17.29062e-5
MA0025.10.0563
MA0027.10.96
MA0028.11.72707e-4
MA0029.10.123
MA0030.10.156
MA0031.10.0177
MA0035.20.00892
MA0038.18.88441e-6
MA0039.24.37188e-4
MA0040.10.395
MA0041.10.865
MA0042.10.797
MA0043.10.539
MA0046.13.26501e-7
MA0047.28.03824e-5
MA0048.10.537
MA0050.10.00932
MA0051.10.00864
MA0052.10.23
MA0055.10.0037
MA0057.10.647
MA0058.17.47392e-4
MA0059.10.0026
MA0060.18.70942e-11
MA0061.10.734
MA0062.25.08405e-6
MA0065.21.80624e-4
MA0066.10.978
MA0067.10.607
MA0068.10.127
MA0069.10.902
MA0070.10.0359
MA0071.10.659
MA0072.10.916
MA0073.10.932
MA0074.10.656
MA0076.10.00172
MA0077.10.0985
MA0078.10.957
MA0079.20.7
MA0080.20.162
MA0081.10.116
MA0083.19.45172e-5
MA0084.10.647
MA0087.10.862
MA0088.10.0991
MA0090.10.716
MA0091.10.0567
MA0092.10.765
MA0093.10.00339
MA0099.21.13119e-5
MA0100.10.735
MA0101.10.285
MA0102.20.568
MA0103.11.50543e-10
MA0104.20.00303
MA0105.10.373
MA0106.10.833
MA0107.10.392
MA0108.20.0121
MA0111.10.223
MA0112.20.0318
MA0113.10.561
MA0114.13.37396e-5
MA0115.10.00295
MA0116.10.872
MA0117.10.249
MA0119.10.0259
MA0122.10.526
MA0124.10.0964
MA0125.10.0373
MA0131.10.753
MA0135.10.868
MA0136.10.91
MA0137.20.689
MA0138.20.126
MA0139.10.0364
MA0140.10.0699
MA0141.10.0185
MA0142.10.551
MA0143.10.268
MA0144.10.594
MA0145.10.157
MA0146.10.0058
MA0147.10.00415
MA0148.13.19763e-4
MA0149.10.0111
MA0150.10.328
MA0152.10.363
MA0153.12.52539e-6
MA0154.10.76
MA0155.10.43
MA0156.10.256
MA0157.10.192
MA0159.10.0026
MA0160.10.00523
MA0162.10.585
MA0163.10.473
MA0164.10.149
MA0258.10.0917
MA0259.10.152



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: CNhs10753

Novel motifP-value
10.148
100.29
1000.534
1010.777
1020.285
1030.903
1040.757
1050.219
1060.343
1070.669
1080.773
1090.0124
110.343
1100.152
1110.935
1120.943
1130.257
1140.755
1150.794
1160.289
1170.107
1180.332
1190.195
120.149
1200.467
1210.667
1220.0899
1230.175
1240.471
1250.955
1260.248
1270.561
1280.757
1290.052
130.00268
1300.681
1310.127
1320.972
1330.0844
1340.433
1350.0352
1360.443
1370.872
1380.614
1390.32
140.721
1400.228
1410.391
1420.118
1430.379
1440.0947
1450.985
1460.36
1470.783
1480.286
1490.876
150.169
1500.38
1510.456
1520.773
1530.601
1540.956
1550.561
1560.226
1570.809
1580.461
1590.962
160.387
1600.56
1610.929
1620.766
1630.719
1640.754
1650.956
1660.437
1670.272
1680.935
1690.012
170.273
180.607
190.816
20.918
200.502
210.989
220.586
230.826
240.0901
250.454
260.032
270.921
280.504
290.183
30.665
300.758
310.915
320.0249
330.0591
340.591
350.721
360.0339
370.388
380.241
390.463
40.268
400.0203
410.219
420.547
430.484
440.816
450.976
460.489
470.0982
480.24
490.263
50.937
500.317
510.894
520.693
530.731
540.969
550.674
560.44
570.292
580.767
590.797
60.674
600.368
610.191
620.8
630.178
640.215
650.578
662.03208e-4
670.346
680.0176
690.0484
70.127
700.626
710.273
720.714
730.247
740.143
750.206
760.407
770.338
780.0385
790.0675
80.369
800.564
810.139
820.0373
830.524
840.414
850.228
860.974
870.0585
880.868
890.388
90.569
900.618
910.36
920.897
930.0937
940.611
950.0466
960.693
970.0681
980.109
990.717



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: CNhs10753


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)
3493 (signet ring cell adenocarcinoma)
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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