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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=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100669
|fonse_cell_line=FF:0100669
|fonse_cell_line_closure=FF:0100669
|fonse_cell_line_closure=FF:0100669

Revision as of 16:49, 29 March 2012


Name:embryonic pancreas cell line:1B2C6
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
age19 week embryo
cell typeunclassifiable
cell line1B2C6
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-1.242954e-4
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-lymphoma0.243
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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: CNhs11731

Jaspar motifP-value
MA0002.20.72
MA0003.10.992
MA0004.10.00183
MA0006.10.764
MA0007.10.162
MA0009.10.892
MA0014.10.34
MA0017.10.709
MA0018.20.624
MA0019.10.463
MA0024.15.9582e-4
MA0025.10.998
MA0027.10.35
MA0028.10.138
MA0029.10.0424
MA0030.10.0678
MA0031.10.466
MA0035.20.014
MA0038.10.927
MA0039.20.0225
MA0040.10.735
MA0041.10.463
MA0042.10.342
MA0043.10.412
MA0046.10.049
MA0047.20.021
MA0048.10.351
MA0050.10.00766
MA0051.10.72
MA0052.10.899
MA0055.10.0473
MA0057.10.945
MA0058.10.041
MA0059.10.251
MA0060.10.108
MA0061.10.314
MA0062.20.678
MA0065.20.303
MA0066.10.337
MA0067.10.604
MA0068.10.0492
MA0069.10.565
MA0070.10.532
MA0071.10.92
MA0072.10.315
MA0073.10.918
MA0074.10.861
MA0076.10.64
MA0077.10.153
MA0078.10.409
MA0079.20.402
MA0080.20.018
MA0081.10.555
MA0083.10.33
MA0084.10.87
MA0087.10.444
MA0088.10.707
MA0090.10.242
MA0091.10.0526
MA0092.10.143
MA0093.10.00377
MA0099.24.7538e-13
MA0100.10.692
MA0101.10.257
MA0102.20.182
MA0103.10.375
MA0104.20.0865
MA0105.10.00118
MA0106.10.496
MA0107.10.579
MA0108.20.189
MA0111.10.916
MA0112.20.0262
MA0113.10.312
MA0114.10.256
MA0115.10.0137
MA0116.10.00241
MA0117.10.217
MA0119.10.943
MA0122.10.559
MA0124.10.483
MA0125.10.953
MA0131.10.145
MA0135.10.47
MA0136.10.214
MA0137.20.413
MA0138.20.569
MA0139.10.64
MA0140.10.0407
MA0141.10.901
MA0142.10.639
MA0143.10.611
MA0144.10.459
MA0145.10.345
MA0146.10.73
MA0147.10.056
MA0148.10.0239
MA0149.10.0379
MA0150.10.365
MA0152.10.625
MA0153.10.524
MA0154.10.0355
MA0155.10.364
MA0156.10.363
MA0157.10.783
MA0159.10.931
MA0160.10.305
MA0162.10.204
MA0163.10.00106
MA0164.10.508
MA0258.10.195
MA0259.10.253



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: CNhs11731

Novel motifP-value
10.227
100.2
1000.744
1010.631
1020.156
1030.47
1040.93
1050.302
1060.0517
1070.79
1080.956
1090.582
110.0194
1100.298
1110.177
1120.189
1130.0817
1140.71
1150.497
1160.314
1170.859
1180.502
1190.723
120.453
1200.568
1210.822
1220.186
1230.745
1240.527
1250.448
1260.919
1270.782
1280.0653
1290.453
130.87
1300.00938
1310.0131
1320.479
1330.0592
1340.116
1350.00197
1360.319
1370.326
1380.708
1390.623
140.78
1400.353
1410.776
1420.528
1430.807
1440.235
1450.338
1460.981
1470.0717
1480.613
1490.148
150.104
1500.689
1510.555
1520.921
1530.41
1540.595
1550.342
1560.86
1570.162
1580.904
1590.878
160.437
1600.249
1610.621
1620.726
1630.933
1640.209
1650.988
1660.309
1670.349
1680.636
1690.245
170.701
180.966
190.0411
20.19
200.0848
210.735
220.612
230.501
240.787
250.245
260.234
270.166
280.457
290.0773
30.136
300.894
310.352
324.9331e-5
330.339
340.722
350.116
360.585
370.142
380.796
390.357
40.173
400.301
410.735
420.679
430.151
440.0646
450.662
460.0523
470.431
480.42
490.543
50.291
500.274
510.85
520.508
530.141
540.919
550.844
560.495
570.298
580.0258
590.0317
60.0925
600.235
610.249
620.00267
630.909
640.301
650.472
660.0164
670.424
680.714
690.961
70.773
700.583
710.0506
720.00753
730.834
740.299
750.476
760.721
770.0525
780.984
790.00255
80.441
800.987
810.00921
820.111
830.98
840.139
850.0614
860.225
870.356
880.189
890.0401
90.477
900.955
910.00533
920.561
930.419
940.727
950.759
960.305
970.333
980.432
990.916



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: CNhs11731


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

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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