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Revision as of 19:18, 15 May 2017

Name:hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep1
Species:Human (Homo sapiens)
Library ID:CNhs12328
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueliver
dev stageNA
sexmale
age15
cell typehepatocyte
cell lineHepG2
companyNA
collaborationCarrie Davis (Cold spring Harbor Laboratories)
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  SAMD00004811
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12328 CAGE DRX007905 DRR008777
Accession ID Hg19

Library idBAMCTSS
CNhs12328 DRZ000202 DRZ001587
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
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C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
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: CNhs12328

Jaspar motifP-value
MA0002.20.0105
MA0003.10.784
MA0004.10.0732
MA0006.10.519
MA0007.10.667
MA0009.10.526
MA0014.10.225
MA0017.15.79612e-25
MA0018.20.0837
MA0019.10.876
MA0024.12.50171e-6
MA0025.10.589
MA0027.10.436
MA0028.11.33431e-5
MA0029.10.00591
MA0030.10.332
MA0031.10.0508
MA0035.20.0172
MA0038.10.0919
MA0039.20.137
MA0040.10.365
MA0041.10.518
MA0042.10.264
MA0043.10.589
MA0046.11.5911e-74
MA0047.21.41803e-4
MA0048.10.0199
MA0050.10.102
MA0051.10.092
MA0052.10.0213
MA0055.11.90065e-5
MA0057.10.913
MA0058.10.0142
MA0059.10.0539
MA0060.17.73912e-17
MA0061.16.64082e-4
MA0062.26.79845e-5
MA0065.22.01494e-8
MA0066.10.635
MA0067.10.00296
MA0068.10.545
MA0069.10.795
MA0070.10.259
MA0071.10.259
MA0072.10.267
MA0073.10.702
MA0074.10.504
MA0076.11.6637e-5
MA0077.10.0589
MA0078.10.545
MA0079.20.646
MA0080.22.68846e-9
MA0081.10.147
MA0083.10.0214
MA0084.10.34
MA0087.10.463
MA0088.10.11
MA0090.10.964
MA0091.10.0419
MA0092.10.0685
MA0093.10.035
MA0099.21.66721e-9
MA0100.10.105
MA0101.10.169
MA0102.20.34
MA0103.10.037
MA0104.20.00991
MA0105.10.00137
MA0106.10.0212
MA0107.10.0134
MA0108.20.123
MA0111.10.797
MA0112.20.768
MA0113.10.958
MA0114.12.76165e-34
MA0115.11.23559e-8
MA0116.10.5
MA0117.10.341
MA0119.10.048
MA0122.10.315
MA0124.10.624
MA0125.10.369
MA0131.10.128
MA0135.10.538
MA0136.19.37614e-5
MA0137.20.203
MA0138.20.489
MA0139.10.00751
MA0140.10.018
MA0141.14.68434e-5
MA0142.10.913
MA0143.10.768
MA0144.10.185
MA0145.10.213
MA0146.10.00208
MA0147.10.0141
MA0148.12.44163e-4
MA0149.10.29
MA0150.10.00656
MA0152.10.204
MA0153.12.86996e-47
MA0154.10.258
MA0155.10.935
MA0156.10.0116
MA0157.10.259
MA0159.10.186
MA0160.10.0103
MA0162.10.899
MA0163.10.0854
MA0164.10.409
MA0258.10.75
MA0259.10.0601



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: CNhs12328

Novel motifP-value
10.438
100.553
1000.0352
1010.326
1020.161
1030.767
1040.695
1050.937
1060.0139
1070.576
1080.427
1090.0825
110.752
1100.919
1110.698
1120.172
1130.0935
1140.368
1150.642
1160.883
1170.124
1180.347
1190.89
120.603
1200.382
1210.58
1220.867
1230.394
1240.174
1250.483
1260.581
1270.34
1280.0128
1290.785
131.06797e-4
1300.813
1310.0261
1320.571
1330.00841
1340.402
1350.0394
1360.0132
1370.00231
1380.379
1390.227
140.0662
1400.7
1410.222
1420.748
1430.129
1440.437
1450.645
1460.904
1470.575
1480.893
1490.784
150.933
1500.53
1510.727
1520.996
1530.344
1540.138
1550.279
1560.884
1570.485
1580.991
1590.678
160.716
1600.752
1610.929
1620.801
1630.704
1640.999
1650.724
1660.352
1670.989
1680.231
1690.287
170.705
180.0495
190.808
20.086
200.17
210.406
220.544
230.00327
240.855
250.613
260.0565
270.22
280.955
290.214
30.996
300.676
310.787
320.246
330.295
340.439
350.891
360.153
370.77
380.871
390.879
40.912
400.00695
410.063
420.348
430.864
440.14
450.981
460.674
470.292
480.545
490.869
50.41
500.203
510.711
520.394
530.337
540.809
550.276
560.847
570.982
580.598
590.491
60.313
600.292
610.112
620.225
630.959
640.855
650.055
660.00947
670.341
680.19
690.436
70.0472
700.134
710.484
720.138
730.139
740.103
750.00138
760.653
770.964
780.0187
790.0186
80.792
800.0473
810.167
820.0837
830.113
840.143
850.0437
860.798
870.0638
880.444
890.404
90.0648
900.593
910.0146
920.0753
930.774
940.0751
950.00291
960.329
970.687
980.877
990.224



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: CNhs12328


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)
0002371 (somatic cell)
0000181 (metabolising cell)
0000417 (endopolyploid cell)
0000668 (parenchymal cell)
0000412 (polyploid cell)
0000255 (eukaryotic cell)
0000182 (hepatocyte)

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

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0101120 (epithelial cell line sample)
0100224 (liver cell line sample)
0100578 (hepatoma cell line sample)
0100599 (Hep-G2 cell 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
CL:0000134 (mesenchymal cell)
CL:0000223 (endodermal cell)
UBERON:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)