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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:1C3D3
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 line1C3D3
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-penis0.0156
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-lymphoma0.099
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11732

Jaspar motifP-value
MA0002.20.519
MA0003.10.605
MA0004.10.0431
MA0006.10.919
MA0007.10.0993
MA0009.10.69
MA0014.10.25
MA0017.10.963
MA0018.20.111
MA0019.10.994
MA0024.10.934
MA0025.10.342
MA0027.10.635
MA0028.10.00944
MA0029.10.363
MA0030.10.0957
MA0031.10.589
MA0035.20.152
MA0038.10.185
MA0039.20.0132
MA0040.10.389
MA0041.10.501
MA0042.10.825
MA0043.10.137
MA0046.10.655
MA0047.20.153
MA0048.10.00643
MA0050.13.55894e-5
MA0051.10.504
MA0052.10.449
MA0055.13.9696e-5
MA0057.10.799
MA0058.10.203
MA0059.10.0385
MA0060.10.023
MA0061.10.31
MA0062.20.229
MA0065.20.0138
MA0066.10.964
MA0067.10.409
MA0068.10.0218
MA0069.10.824
MA0070.10.91
MA0071.10.153
MA0072.10.633
MA0073.10.696
MA0074.10.823
MA0076.10.14
MA0077.10.231
MA0078.10.56
MA0079.20.983
MA0080.21.414e-5
MA0081.10.196
MA0083.10.17
MA0084.10.749
MA0087.10.941
MA0088.10.044
MA0090.10.409
MA0091.10.0218
MA0092.10.0657
MA0093.10.041
MA0099.21.89421e-6
MA0100.10.987
MA0101.10.0199
MA0102.20.0395
MA0103.10.348
MA0104.20.00717
MA0105.10.944
MA0106.10.83
MA0107.10.128
MA0108.23.59254e-4
MA0111.10.385
MA0112.20.926
MA0113.10.433
MA0114.10.0378
MA0115.10.483
MA0116.10.451
MA0117.10.0647
MA0119.10.167
MA0122.10.367
MA0124.10.177
MA0125.10.558
MA0131.10.329
MA0135.10.0751
MA0136.10.00624
MA0137.20.125
MA0138.20.813
MA0139.10.0777
MA0140.10.0977
MA0141.10.129
MA0142.10.0538
MA0143.10.897
MA0144.10.559
MA0145.10.302
MA0146.10.519
MA0147.17.01999e-4
MA0148.10.0173
MA0149.10.0152
MA0150.10.583
MA0152.10.619
MA0153.10.48
MA0154.10.428
MA0155.10.394
MA0156.10.798
MA0157.10.672
MA0159.10.0515
MA0160.10.682
MA0162.10.746
MA0163.10.892
MA0164.10.203
MA0258.10.865
MA0259.10.0627



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: CNhs11732

Novel motifP-value
10.579
100.292
1000.278
1010.891
1020.128
1030.121
1040.449
1050.891
1060.00278
1070.564
1080.869
1090.0174
110.547
1100.719
1110.114
1120.446
1130.0437
1140.646
1150.871
1160.845
1170.0779
1180.342
1190.0845
120.287
1200.163
1210.493
1220.948
1230.363
1240.237
1250.768
1260.667
1270.716
1280.0382
1290.219
130.114
1300.673
1310.105
1320.677
1330.109
1340.0438
1350.0191
1360.118
1370.334
1380.583
1390.542
140.715
1400.74
1410.829
1420.266
1430.458
1440.914
1450.136
1460.697
1470.054
1480.68
1490.11
150.0264
1500.978
1510.991
1520.817
1530.438
1540.506
1550.179
1560.598
1570.866
1580.129
1590.225
160.854
1600.831
1610.295
1620.802
1630.588
1640.611
1650.536
1660.324
1670.145
1680.985
1690.573
170.47
180.779
190.179
20.0436
200.00712
210.256
220.503
230.465
240.873
250.195
260.409
270.106
280.554
290.694
30.43
300.131
310.336
320.085
330.937
340.642
350.706
360.0852
370.642
380.497
390.846
40.988
400.0278
410.247
420.174
430.782
440.909
450.675
460.696
470.623
480.454
490.729
50.713
500.175
510.857
520.0316
530.341
540.909
550.448
560.416
570.251
580.518
590.143
60.536
600.0982
610.042
620.226
630.286
640.661
650.936
660.122
670.298
680.887
690.569
70.591
700.0593
710.85
720.104
730.618
740.472
750.199
760.0726
770.739
780.8
790.648
80.608
800.642
810.0985
820.504
830.572
840.791
850.834
860.437
870.103
880.822
890.0333
90.399
900.145
910.128
920.413
930.0195
940.631
950.147
960.272
970.761
980.371
990.229



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: CNhs11732


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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