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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000160,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,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:0003928,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004458,UBERON:0004921,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0007026,UBERON:0007329,UBERON:0009142
|ancestors_in_anatomy_facet=UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000160,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,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:0003928,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004458,UBERON:0004921,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0007026,UBERON:0007329,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:0101120
|fonse_cell_line=FF:0101120
|fonse_cell_line_closure=FF:0101120
|fonse_cell_line_closure=FF:0101120

Revision as of 16:41, 29 March 2012


Name:ductal cell carcinoma cell line:MIA Paca2
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
age65
cell typeduct cell
cell lineMIA Paca2
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-penis0.238
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-lymphoma0.24
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
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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: CNhs11259

Jaspar motifP-value
MA0002.20.00856
MA0003.10.0737
MA0004.10.1
MA0006.10.752
MA0007.10.816
MA0009.10.673
MA0014.10.0774
MA0017.10.78
MA0018.20.093
MA0019.10.122
MA0024.10.0652
MA0025.10.69
MA0027.10.329
MA0028.14.54187e-7
MA0029.10.406
MA0030.10.913
MA0031.10.858
MA0035.20.43
MA0038.10.759
MA0039.20.0654
MA0040.10.56
MA0041.10.319
MA0042.10.686
MA0043.10.209
MA0046.10.145
MA0047.20.197
MA0048.10.0545
MA0050.10.0427
MA0051.10.159
MA0052.10.0669
MA0055.11.12894e-4
MA0057.10.517
MA0058.10.0147
MA0059.10.0639
MA0060.10.363
MA0061.10.0267
MA0062.27.63894e-7
MA0065.20.279
MA0066.10.645
MA0067.10.423
MA0068.19.24016e-5
MA0069.10.883
MA0070.10.102
MA0071.10.261
MA0072.10.996
MA0073.10.473
MA0074.10.463
MA0076.14.74145e-8
MA0077.10.928
MA0078.10.684
MA0079.20.685
MA0080.28.40022e-10
MA0081.10.216
MA0083.10.212
MA0084.10.281
MA0087.10.222
MA0088.10.00453
MA0090.10.475
MA0091.10.00438
MA0092.10.0604
MA0093.10.0265
MA0099.20.12
MA0100.10.365
MA0101.10.0877
MA0102.20.643
MA0103.10.365
MA0104.20.011
MA0105.10.0229
MA0106.10.511
MA0107.10.00844
MA0108.24.09946e-4
MA0111.10.721
MA0112.20.108
MA0113.10.348
MA0114.10.421
MA0115.10.484
MA0116.10.443
MA0117.10.689
MA0119.10.0751
MA0122.10.928
MA0124.10.582
MA0125.10.801
MA0131.10.037
MA0135.10.862
MA0136.11.34985e-5
MA0137.20.226
MA0138.20.325
MA0139.10.816
MA0140.10.875
MA0141.10.722
MA0142.10.278
MA0143.10.328
MA0144.10.0133
MA0145.10.567
MA0146.10.0163
MA0147.10.0144
MA0148.10.262
MA0149.10.05
MA0150.10.193
MA0152.10.868
MA0153.10.169
MA0154.10.0731
MA0155.10.109
MA0156.10.238
MA0157.10.119
MA0159.10.106
MA0160.10.886
MA0162.10.255
MA0163.10.359
MA0164.10.875
MA0258.10.306
MA0259.10.0951



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: CNhs11259

Novel motifP-value
10.426
100.244
1000.031
1010.638
1020.652
1030.304
1040.539
1050.631
1061.34347e-4
1070.00902
1080.873
1090.167
110.792
1100.673
1110.707
1120.675
1130.0265
1140.752
1150.726
1160.946
1170.0774
1180.183
1190.145
120.233
1200.381
1210.737
1220.879
1230.245
1240.0962
1250.899
1260.905
1270.565
1287.94282e-4
1290.484
130.00242
1300.341
1310.558
1320.631
1330.359
1340.463
1355.48211e-4
1360.219
1370.382
1380.805
1390.7
140.841
1400.13
1410.435
1420.499
1430.0319
1440.771
1450.236
1460.0902
1470.761
1480.513
1490.168
150.942
1500.321
1510.553
1520.701
1530.947
1540.933
1550.964
1560.308
1570.678
1580.694
1590.472
160.908
1600.134
1610.804
1620.635
1630.977
1640.0718
1650.977
1660.327
1670.0992
1680.227
1690.268
170.43
180.684
190.228
20.0449
200.0179
210.104
220.518
230.0156
240.711
250.738
260.882
270.099
280.395
290.198
30.679
300.225
310.298
320.0206
330.214
340.191
350.641
360.0922
370.503
380.873
390.752
40.197
400.397
410.0076
420.589
430.355
440.688
450.153
460.637
470.425
480.466
490.537
50.476
500.608
510.35
520.0239
530.618
540.353
550.712
560.826
570.494
580.39
590.114
60.805
600.089
610.425
620.32
630.866
640.778
650.124
660.179
670.634
680.0289
690.802
70.852
700.518
710.996
720.44
730.274
740.514
750.0294
760.0378
770.428
780.546
790.0647
80.515
800.046
810.342
820.62
830.332
840.813
850.152
860.956
870.0886
880.808
890.282
90.0412
900.841
910.0419
920.394
930.286
940.335
950.0805
960.64
970.859
980.488
990.597



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: CNhs11259


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)
305 (carcinoma)
3498 (pancreatic ductal adenocarcinoma)
4 (disease)
4074 (pancreas adenocarcinoma)
4905 (pancreatic carcinoma)

UBERON: Anatomy
0000058 (duct)
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)
0000477 (anatomical cluster)
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)
0003928 (digestive system duct)
0004111 (anatomical conduit)
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)
0007329 (pancreatic duct)
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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