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{{f5samples
{{f5samples
|F5samples=
|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_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_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: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

Revision as of 16:55, 29 March 2012


Name:pancreatic carcinoma cell line:NOR-P1
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
sexunknown
ageNA
cell typeunclassifiable
cell lineNOR-P1
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-penis0.338
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-lymphoma0.434
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: CNhs11832

Jaspar motifP-value
MA0002.20.0678
MA0003.10.881
MA0004.10.135
MA0006.10.849
MA0007.10.71
MA0009.10.858
MA0014.10.396
MA0017.10.768
MA0018.20.5
MA0019.10.0142
MA0024.10.00494
MA0025.10.063
MA0027.10.916
MA0028.10.0349
MA0029.10.742
MA0030.10.915
MA0031.10.419
MA0035.20.00824
MA0038.10.921
MA0039.20.00774
MA0040.10.535
MA0041.10.269
MA0042.10.498
MA0043.10.522
MA0046.10.556
MA0047.20.454
MA0048.10.178
MA0050.12.71472e-7
MA0051.11.75127e-4
MA0052.10.0077
MA0055.10.00126
MA0057.10.677
MA0058.10.148
MA0059.10.0677
MA0060.10.51
MA0061.10.0386
MA0062.20.449
MA0065.20.0178
MA0066.10.82
MA0067.10.125
MA0068.10.979
MA0069.10.996
MA0070.10.126
MA0071.10.192
MA0072.10.504
MA0073.10.885
MA0074.10.862
MA0076.10.358
MA0077.10.412
MA0078.10.629
MA0079.20.441
MA0080.21.02569e-6
MA0081.10.0159
MA0083.10.0123
MA0084.10.701
MA0087.10.687
MA0088.10.0297
MA0090.10.0698
MA0091.10.521
MA0092.10.581
MA0093.10.146
MA0099.28.71502e-5
MA0100.10.938
MA0101.10.024
MA0102.20.515
MA0103.11.38567e-4
MA0104.20.0292
MA0105.10.716
MA0106.10.287
MA0107.10.00422
MA0108.28.42506e-7
MA0111.10.45
MA0112.20.415
MA0113.10.974
MA0114.10.0168
MA0115.10.204
MA0116.10.47
MA0117.10.74
MA0119.10.53
MA0122.10.813
MA0124.10.785
MA0125.10.594
MA0131.10.228
MA0135.10.00555
MA0136.16.01921e-6
MA0137.20.0176
MA0138.20.0406
MA0139.10.875
MA0140.10.0818
MA0141.10.702
MA0142.10.624
MA0143.10.852
MA0144.10.146
MA0145.10.73
MA0146.10.272
MA0147.10.0222
MA0148.10.468
MA0149.10.181
MA0150.10.378
MA0152.10.208
MA0153.10.236
MA0154.10.992
MA0155.10.398
MA0156.10.0104
MA0157.10.831
MA0159.10.702
MA0160.10.947
MA0162.10.802
MA0163.10.169
MA0164.10.979
MA0258.10.128
MA0259.10.0543



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: CNhs11832

Novel motifP-value
10.0442
100.345
1000.0426
1010.248
1020.668
1030.136
1040.309
1050.998
1060.902
1070.425
1080.339
1090.162
110.494
1100.131
1110.408
1120.544
1130.153
1140.838
1150.937
1160.626
1170.0359
1180.181
1190.137
120.989
1200.685
1210.962
1220.998
1231.46031e-4
1240.839
1250.735
1260.824
1270.34
1280.846
1290.871
130.00263
1300.954
1310.599
1320.817
1335.29346e-4
1340.49
1350.0605
1360.0466
1370.0471
1380.765
1390.332
140.479
1400.164
1410.293
1420.946
1430.0584
1440.557
1450.85
1460.547
1470.524
1480.645
1490.908
150.67
1500.881
1510.599
1520.294
1530.748
1540.493
1550.407
1560.362
1570.239
1580.651
1590.875
160.267
1600.788
1610.506
1620.222
1630.465
1640.44
1650.521
1660.429
1670.299
1680.147
1690.393
170.346
180.921
190.57
20.203
200.14
210.138
220.829
230.603
240.794
250.492
260.0472
270.468
280.796
290.197
30.402
300.484
310.905
320.4
330.741
340.468
350.798
360.0751
370.628
380.625
390.417
40.707
400.0744
410.0954
420.391
430.675
440.692
450.882
460.493
470.212
480.291
490.101
50.947
500.83
510.794
520.843
530.0874
540.861
550.979
560.751
570.016
580.315
590.385
60.204
600.85
610.318
620.328
630.887
640.414
650.666
660.307
670.657
680.206
690.431
70.0789
700.571
710.372
720.981
730.611
740.428
750.211
760.0386
770.789
780.00216
790.252
80.86
800.109
810.897
820.924
830.998
840.315
850.991
860.493
870.28
880.721
890.0747
90.105
900.256
910.323
920.638
930.491
940.835
950.199
960.947
970.724
980.678
990.968



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: CNhs11832


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)
10165 (endocrine pancreas cancer)
14566 (disease of cellular proliferation)
162 (cancer)
170 (endocrine gland cancer)
1793 (pancreatic cancer)
1798 (pancreatic endocrine carcinoma)
1799 (islet cell tumor)
305 (carcinoma)
4 (disease)

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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