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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005854
|DRA_sample_Accession=CAGE@SAMD00005854
|accession_numbers=CAGE;DRX007874;DRR008746;DRZ000171;DRZ001556
|accession_numbers=CAGE;DRX007874;DRR008746;DRZ000171;DRZ001556;DRZ011521;DRZ012906
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0001264,UBERON:0002100,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002323,UBERON:0005177,UBERON:0000464,UBERON:0004458,UBERON:0000949
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0001264,UBERON:0002100,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002323,UBERON:0005177,UBERON:0000464,UBERON:0004458,UBERON:0000949
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/embryonic%2520pancreas%2520cell%2520line%253a1C3IKEI.CNhs11733.10606-108F3.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/embryonic%2520pancreas%2520cell%2520line%253a1C3IKEI.CNhs11733.10606-108F3.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/embryonic%2520pancreas%2520cell%2520line%253a1C3IKEI.CNhs11733.10606-108F3.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/embryonic%2520pancreas%2520cell%2520line%253a1C3IKEI.CNhs11733.10606-108F3.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/embryonic%2520pancreas%2520cell%2520line%253a1C3IKEI.CNhs11733.10606-108F3.hg38.nobarcode.ctss.bed.gz
|id=FF:10606-108F3
|id=FF:10606-108F3
|is_a=EFO:0002091;;FF:0000210;;FF:0100669;;UBERON:0001264
|is_a=EFO:0002091;;FF:0000210;;FF:0100669;;UBERON:0001264
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|library_id=CNhs11733
|library_id=CNhs11733
|library_id_phase_based=2:CNhs11733
|library_id_phase_based=2:CNhs11733
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10606
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10606
|name=embryonic pancreas cell line:1C3IKEI
|name=embryonic pancreas cell line:1C3IKEI
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
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|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 89: Line 99:
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10606-108F3;search_select_hide=table117:FF:10606-108F3
}}
}}

Latest revision as of 14:30, 3 June 2020

Name:embryonic pancreas cell line:1C3IKEI
Species:Human (Homo sapiens)
Library ID:CNhs11733
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuepancreas
dev stageNA
sexunknown
age19 week embryo
cell typeunclassifiable
cell line1C3IKEI
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005854
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11733 CAGE DRX007874 DRR008746
Accession ID Hg19

Library idBAMCTSS
CNhs11733 DRZ000171 DRZ001556
Accession ID Hg38

Library idBAMCTSS
CNhs11733 DRZ011521 DRZ012906
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload


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-0.068
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-lymphoma0.183
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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



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: CNhs11733

Jaspar motifP-value
MA0002.20.784
MA0003.10.736
MA0004.10.0203
MA0006.10.857
MA0007.10.67
MA0009.10.958
MA0014.10.295
MA0017.10.996
MA0018.20.539
MA0019.10.972
MA0024.10.0132
MA0025.10.955
MA0027.10.411
MA0028.10.00157
MA0029.10.0149
MA0030.10.0202
MA0031.10.3
MA0035.20.135
MA0038.10.514
MA0039.20.0301
MA0040.10.889
MA0041.10.291
MA0042.10.462
MA0043.10.4
MA0046.10.409
MA0047.20.0306
MA0048.10.127
MA0050.10.0061
MA0051.10.977
MA0052.10.47
MA0055.10.00183
MA0057.10.558
MA0058.10.0666
MA0059.10.6
MA0060.10.171
MA0061.10.348
MA0062.24.9463e-4
MA0065.20.721
MA0066.10.221
MA0067.10.515
MA0068.10.244
MA0069.10.565
MA0070.10.259
MA0071.10.851
MA0072.10.186
MA0073.10.998
MA0074.10.702
MA0076.10.00115
MA0077.10.272
MA0078.10.876
MA0079.20.23
MA0080.20.164
MA0081.10.504
MA0083.10.418
MA0084.10.706
MA0087.10.24
MA0088.10.847
MA0090.10.201
MA0091.10.00543
MA0092.10.12
MA0093.10.0154
MA0099.22.39227e-18
MA0100.10.873
MA0101.10.237
MA0102.20.814
MA0103.10.75
MA0104.20.202
MA0105.13.34915e-4
MA0106.10.462
MA0107.10.564
MA0108.20.137
MA0111.10.779
MA0112.20.00845
MA0113.10.137
MA0114.10.521
MA0115.10.0837
MA0116.10.00352
MA0117.10.181
MA0119.10.651
MA0122.10.385
MA0124.11
MA0125.10.785
MA0131.10.967
MA0135.10.824
MA0136.10.979
MA0137.20.973
MA0138.20.328
MA0139.10.888
MA0140.10.158
MA0141.10.979
MA0142.10.381
MA0143.10.23
MA0144.10.639
MA0145.10.284
MA0146.10.821
MA0147.10.16
MA0148.10.06
MA0149.10.0456
MA0150.10.171
MA0152.10.679
MA0153.10.66
MA0154.10.0157
MA0155.10.286
MA0156.10.012
MA0157.10.854
MA0159.10.969
MA0160.10.657
MA0162.10.113
MA0163.18.19239e-4
MA0164.10.387
MA0258.10.0492
MA0259.10.416



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: CNhs11733

Novel motifP-value
10.189
100.222
1000.786
1010.552
1020.207
1030.727
1040.872
1050.954
1060.00171
1070.277
1080.284
1090.61
110.037
1100.229
1110.86
1120.0873
1130.0334
1140.325
1150.725
1160.115
1170.772
1180.322
1190.762
120.718
1200.397
1210.982
1220.143
1230.52
1240.273
1250.0853
1260.453
1270.908
1280.00229
1290.623
130.937
1300.0231
1310.103
1320.354
1330.208
1340.155
1350.0049
1360.304
1370.441
1380.683
1390.831
140.89
1400.296
1410.794
1420.537
1430.248
1440.318
1450.234
1460.89
1470.239
1480.481
1490.0696
150.406
1500.52
1510.478
1520.974
1530.329
1540.697
1550.157
1560.819
1570.603
1580.473
1590.688
160.24
1600.0957
1610.728
1620.418
1630.624
1640.138
1650.689
1660.115
1670.812
1680.798
1690.139
170.475
180.611
190.0571
20.223
200.0405
210.972
220.5
230.184
240.358
250.329
260.0275
270.0414
280.633
290.237
30.184
300.73
310.268
324.76787e-5
330.386
340.868
350.0556
360.584
370.192
380.57
390.441
40.299
400.752
410.474
420.983
430.101
440.0192
450.836
460.042
470.255
480.368
490.169
50.187
500.501
510.576
520.211
530.357
540.505
550.743
560.934
570.949
580.148
590.0329
60.21
600.0759
610.179
620.0192
630.536
640.143
650.206
660.0484
670.192
680.604
690.265
70.462
700.198
710.0453
720.0761
730.754
740.224
750.67
760.43
770.0972
780.834
790.00713
80.103
800.467
810.00943
820.0851
830.624
840.207
850.0231
860.423
870.252
880.105
890.0151
90.526
900.867
910.00693
920.0838
930.302
940.25
950.908
960.19
970.151
980.911
990.759



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: CNhs11733


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
0000468 (multi-cellular organism)
0000922 (embryo)
0001264 (pancreas)
0002100 (trunk)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002323 (body cavity)
0005177 (trunk region element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0000949 (endocrine system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100669 (embryonic cell line sample)

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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