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{{f5samples
{{f5samples
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|DRA_sample_Accession=CAGE@SAMD00005404
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|accession_numbers=CAGE;DRX007783;DRR008655;DRZ000080;DRZ001465;DRZ011430;DRZ012815
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255
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|fonse_treatment_closure=FF:0000343,FF:0011132,FF:11899-125E9
|fonse_treatment_closure=FF:0000343,FF:0011132,FF:11899-125E9
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|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/Hep-2%2520cells%2520mock%2520treated%252c%2520biol_rep2.CNhs13500.11899-125E9.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/Hep-2%2520cells%2520mock%2520treated%252c%2520biol_rep2.CNhs13500.11899-125E9.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/Hep-2%2520cells%2520mock%2520treated%252c%2520biol_rep2.CNhs13500.11899-125E9.hg38.nobarcode.bam
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|id=FF:11899-125E9
|id=FF:11899-125E9
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|library_id=CNhs13500
|library_id=CNhs13500
|library_id_phase_based=2:CNhs13500
|library_id_phase_based=2:CNhs13500
|microRNAs=
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|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11899
|name=Hep-2 cells mock treated, biol_rep2
|name=Hep-2 cells mock treated, biol_rep2
|namespace=
|namespace=
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|profile_rnaseq=
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11899-125E9;search_select_hide=table117:FF:11899-125E9
}}
}}

Latest revision as of 18:27, 4 June 2020

Name:Hep-2 cells mock treated, biol_rep2
Species:Human (Homo sapiens)
Library ID:CNhs13500
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
age56
cell typeunclassifiable
cell lineHep-2
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3b
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005404
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13500 CAGE DRX007783 DRR008655
Accession ID Hg19

Library idBAMCTSS
CNhs13500 DRZ000080 DRZ001465
Accession ID Hg38

Library idBAMCTSS
CNhs13500 DRZ011430 DRZ012815
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-0.0107
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
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: CNhs13500

Jaspar motifP-value
MA0002.20.0478
MA0003.10.98
MA0004.10.13
MA0006.10.435
MA0007.10.152
MA0009.10.788
MA0014.10.752
MA0017.10.697
MA0018.20.94
MA0019.10.866
MA0024.17.48717e-9
MA0025.10.186
MA0027.10.79
MA0028.11.24733e-5
MA0029.10.737
MA0030.10.397
MA0031.10.187
MA0035.20.427
MA0038.10.952
MA0039.20.0291
MA0040.10.269
MA0041.10.342
MA0042.10.513
MA0043.10.0424
MA0046.10.417
MA0047.20.852
MA0048.10.0981
MA0050.10.0421
MA0051.10.62
MA0052.10.00441
MA0055.11.49238e-4
MA0057.10.174
MA0058.10.0761
MA0059.10.0201
MA0060.10.0425
MA0061.10.0195
MA0062.20.0122
MA0065.20.0246
MA0066.10.715
MA0067.10.274
MA0068.17.02036e-4
MA0069.10.333
MA0070.10.654
MA0071.10.0915
MA0072.10.717
MA0073.10.238
MA0074.10.887
MA0076.12.2518e-4
MA0077.10.819
MA0078.10.137
MA0079.20.381
MA0080.22.40031e-8
MA0081.10.279
MA0083.10.00156
MA0084.10.405
MA0087.10.551
MA0088.10.0143
MA0090.10.00188
MA0091.10.517
MA0092.10.964
MA0093.10.0792
MA0099.20.00759
MA0100.10.335
MA0101.10.0912
MA0102.20.787
MA0103.10.0252
MA0104.25.54243e-4
MA0105.10.289
MA0106.10.919
MA0107.10.0154
MA0108.20.298
MA0111.10.707
MA0112.20.0586
MA0113.10.865
MA0114.10.0195
MA0115.10.112
MA0116.10.658
MA0117.10.924
MA0119.10.874
MA0122.10.891
MA0124.10.808
MA0125.10.436
MA0131.10.238
MA0135.10.919
MA0136.13.62378e-4
MA0137.20.0266
MA0138.20.0998
MA0139.10.706
MA0140.10.734
MA0141.10.00713
MA0142.10.981
MA0143.10.113
MA0144.10.449
MA0145.10.935
MA0146.10.221
MA0147.13.71407e-4
MA0148.10.304
MA0149.10.0512
MA0150.10.4
MA0152.10.391
MA0153.10.0146
MA0154.10.495
MA0155.10.215
MA0156.10.0608
MA0157.10.128
MA0159.10.176
MA0160.10.0281
MA0162.10.274
MA0163.10.203
MA0164.10.203
MA0258.10.991
MA0259.10.0148



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: CNhs13500

Novel motifP-value
10.148
100.07
1000.0292
1010.272
1020.865
1030.842
1040.769
1050.108
1060.00248
1070.0658
1080.709
1090.00277
110.957
1100.483
1110.619
1120.248
1130.00149
1140.941
1150.956
1160.528
1170.207
1180.143
1190.955
120.871
1200.0532
1210.608
1220.192
1230.121
1240.694
1250.765
1260.838
1270.2
1286.27223e-5
1290.281
131.65776e-4
1300.536
1310.538
1320.591
1330.213
1340.746
1350.107
1360.00446
1370.246
1380.842
1390.0607
140.395
1400.431
1410.23
1420.851
1430.212
1440.296
1450.252
1460.921
1470.822
1480.57
1490.537
150.826
1500.826
1510.511
1520.447
1530.71
1540.437
1550.512
1560.0375
1570.105
1580.149
1590.295
160.946
1600.483
1610.486
1620.827
1630.22
1640.0188
1650.784
1660.0759
1670.218
1680.235
1690.428
170.597
180.153
190.839
20.422
200.139
210.432
220.87
230.00365
240.571
250.36
260.977
270.74
280.844
290.0229
30.524
300.481
310.476
320.0743
330.189
340.192
350.75
360.172
370.653
380.815
390.818
40.242
400.0155
410.0746
420.915
430.312
440.0503
450.163
460.551
470.516
480.552
490.2
50.316
500.902
510.473
520.234
530.0665
540.364
550.0217
560.972
570.822
580.909
590.793
60.739
600.239
610.0643
620.886
630.615
640.759
650.371
660.53
670.855
680.565
690.942
70.0342
700.11
710.0551
720.795
730.562
740.0611
750.207
760.31
770.711
780.217
790.868
80.147
800.0355
810.328
820.1
830.981
840.295
850.0233
860.813
870.00797
880.8
890.703
90.596
900.0195
910.0184
920.0576
930.32
940.391
950.0429
960.46
970.836
980.731
990.359



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: CNhs13500


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)
0000548 (animal cell)
0000066 (epithelial cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
305 (carcinoma)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001737 (larynx)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000072 (segment of respiratory tract)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0001004 (respiratory system)
0001557 (upper respiratory tract)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000343 (control treatment sample)
0000350 (experimentally modified sample)
0104978 (HEp-2 cell sample)
0100297 (carcinoma cell line sample)
0101120 (epithelial cell line sample)
0011132 (human Hep-2 cells mock treated 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
UBERON:0008947 (respiratory primordium)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)

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