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{{f5samples
{{f5samples
|id=FF:10797-110I5
|F5samples=
|name=tubular adenocarcinoma cell line:SUIT-2
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000160,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,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:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004458,UBERON:0004921,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0007026,UBERON:0009142
|sample_id=10797
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|sample_cell_lot=
|sample_cell_catalog=jcrb1094
|sample_company=JAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=pancreas
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=73
|sample_ethnicity=J
|rna_rin=
|rna_od260/230=2.17
|rna_od260/280=2.06
|sample_cell_type=duct cell
|sample_cell_line=SUIT-2
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=tubular adenocarcinoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=82.16869
|rna_concentration=1.74827
|sample_note=
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|profile_srnaseq=,,,
|profile_rnaseq=,,,
|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
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000160,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,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:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004458,UBERON:0004921,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0007026,UBERON:0009142
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:162,DOID:170,DOID:1793,DOID:299,DOID:305,DOID:4,DOID:4929
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:162,DOID:170,DOID:1793,DOID:299,DOID:305,DOID:4,DOID:4929
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0100794,FF:0101120
|fonse_cell_line=FF:0100794,FF:0101120
|fonse_cell_line_closure=FF:0100794,FF:0101120
|fonse_cell_line_closure=FF:0100794,FF:0101120
Line 66: Line 34:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10797-110I5
|is_a=CL:0000083;;DOID:4929;;EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100167;;FF:0103493
|is_a=CL:0000083;;DOID:4929;;EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100167;;FF:0103493
|name=tubular adenocarcinoma cell line:SUIT-2
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11883,LSID830,release010,COMPLETED
|profile_rnaseq=,,,
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|rna_catalog_number=
|rna_concentration=1.74827
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.17
|rna_od260/280=2.06
|rna_position=I5
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=110I5
|rna_weight_ug=82.16869
|sample_age=73
|sample_cell_catalog=jcrb1094
|sample_cell_line=SUIT-2
|sample_cell_lot=
|sample_cell_type=duct cell
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=JAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
|sample_description=
|sample_dev_stage=
|sample_disease=tubular adenocarcinoma
|sample_donor(cell lot)=
|sample_ethnicity=J
|sample_experimental_condition=
|sample_id=10797
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=pancreas
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}}
}}

Revision as of 14:15, 21 March 2012


Name:tubular adenocarcinoma cell line:SUIT-2
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
sexmale
age73
cell typeduct cell
cell lineSUIT-2
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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]





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
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C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
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: CNhs11883

Jaspar motifP-value
MA0002.20.00336
MA0003.10.966
MA0004.10.508
MA0006.10.308
MA0007.10.578
MA0009.10.541
MA0014.10.365
MA0017.10.00181
MA0018.22.77992e-6
MA0019.10.698
MA0024.10.111
MA0025.10.0191
MA0027.10.901
MA0028.15.19852e-4
MA0029.10.391
MA0030.10.00695
MA0031.10.041
MA0035.20.12
MA0038.10.136
MA0039.20.0146
MA0040.10.907
MA0041.10.556
MA0042.10.744
MA0043.10.00657
MA0046.11.17079e-25
MA0047.20.0379
MA0048.10.0478
MA0050.10.15
MA0051.10.00673
MA0052.10.0154
MA0055.10.0219
MA0057.10.212
MA0058.10.974
MA0059.10.548
MA0060.13.34774e-5
MA0061.10.00788
MA0062.20.00647
MA0065.20.193
MA0066.10.11
MA0067.10.165
MA0068.10.433
MA0069.10.471
MA0070.10.551
MA0071.10.997
MA0072.10.549
MA0073.10.615
MA0074.10.972
MA0076.10.00303
MA0077.10.85
MA0078.10.535
MA0079.20.161
MA0080.22.71571e-5
MA0081.10.0547
MA0083.10.796
MA0084.10.611
MA0087.10.334
MA0088.10.299
MA0090.10.716
MA0091.10.0959
MA0092.10.0925
MA0093.10.577
MA0099.20.0915
MA0100.10.1
MA0101.10.0599
MA0102.20.398
MA0103.10.0016
MA0104.20.296
MA0105.11.15877e-4
MA0106.10.67
MA0107.10.0462
MA0108.20.0184
MA0111.10.89
MA0112.20.222
MA0113.10.53
MA0114.11.57499e-5
MA0115.10.127
MA0116.10.00132
MA0117.10.0441
MA0119.10.52
MA0122.10.981
MA0124.10.268
MA0125.10.13
MA0131.10.379
MA0135.10.714
MA0136.10.00635
MA0137.20.397
MA0138.20.259
MA0139.10.941
MA0140.10.715
MA0141.10.38
MA0142.10.644
MA0143.10.784
MA0144.10.614
MA0145.10.955
MA0146.10.181
MA0147.10.564
MA0148.10.00286
MA0149.10.216
MA0150.10.917
MA0152.10.251
MA0153.17.28698e-21
MA0154.10.0135
MA0155.10.327
MA0156.10.364
MA0157.10.494
MA0159.10.425
MA0160.10.69
MA0162.10.925
MA0163.14.05799e-4
MA0164.10.816
MA0258.10.1
MA0259.10.369



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: CNhs11883

Novel motifP-value
10.135
100.376
1000.547
1010.113
1020.777
1030.834
1040.558
1050.308
1060.247
1070.189
1080.475
1090.782
110.0483
1100.723
1110.573
1120.433
1130.00569
1140.446
1150.751
1160.24
1170.646
1180.949
1190.126
120.666
1200.15
1210.725
1220.975
1230.0383
1240.00951
1250.169
1260.439
1270.996
1280.336
1290.776
130.918
1300.967
1310.0135
1320.19
1330.077
1340.0332
1350.029
1360.0665
1370.167
1380.278
1390.677
140.717
1400.714
1410.00352
1420.967
1430.0279
1440.989
1450.52
1460.144
1470.293
1480.948
1490.462
150.847
1500.457
1510.817
1520.015
1530.759
1540.617
1550.517
1560.924
1570.317
1580.572
1590.831
160.314
1600.0285
1610.187
1620.82
1630.345
1640.22
1650.272
1660.966
1670.581
1680.488
1690.486
170.453
180.223
190.101
20.477
200.00957
210.577
220.771
230.127
240.518
250.124
260.742
270.707
280.485
290.359
30.533
300.819
310.406
325.09888e-4
330.256
340.419
350.0426
360.286
370.702
380.447
390.83
40.936
400.818
410.00347
420.919
430.192
440.916
450.869
460.224
470.484
480.407
490.12
50.313
500.235
510.869
520.776
530.292
540.766
550.921
560.353
570.69
580.332
590.109
60.237
600.856
610.628
620.206
630.677
640.243
650.291
660.86
670.0954
680.101
690.621
70.446
700.709
710.0493
720.268
730.00881
740.745
750.998
760.103
770.202
780.384
790.00147
80.783
800.0256
810.0117
820.0569
830.76
840.536
850.679
860.422
870.882
880.122
890.176
90.156
900.265
910.0547
920.343
930.47
940.0425
950.74
960.119
970.594
980.6
990.404



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: CNhs11883


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)
299 (adenocarcinoma)
305 (carcinoma)
4 (disease)
4929 (tubular adenocarcinoma)

UBERON: Anatomy
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)
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)
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)
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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