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|library_id=CNhs12329
|library_id=CNhs12329
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|library_id_phase_based=2:CNhs12329
|name="hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep2"
|name=hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep2
|namespace=FANTOM5
|namespace=FANTOM5
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Revision as of 18:16, 27 November 2014


Name:hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep2
Species:Human (Homo sapiens)
Library ID:CNhs12329
Sample type:cell lines
Genomic View: UCSC
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  SAMD00005169
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12329 CAGE DRX007906 DRR008778
Accession ID Hg19

Library idBAMCTSS
CNhs12329 DRZ000203 DRZ001588
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-penis0.236
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-lymphoma0.573
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs12329

Jaspar motifP-value
MA0002.20.0142
MA0003.10.829
MA0004.10.0736
MA0006.10.378
MA0007.10.592
MA0009.10.533
MA0014.10.225
MA0017.14.05605e-26
MA0018.20.0351
MA0019.10.817
MA0024.11.71008e-6
MA0025.10.569
MA0027.10.607
MA0028.15.50807e-6
MA0029.10.00589
MA0030.10.44
MA0031.10.0719
MA0035.20.0179
MA0038.10.114
MA0039.20.14
MA0040.10.375
MA0041.10.973
MA0042.10.295
MA0043.10.411
MA0046.15.59063e-72
MA0047.23.03635e-4
MA0048.10.0345
MA0050.10.101
MA0051.10.145
MA0052.10.0127
MA0055.14.65199e-5
MA0057.10.956
MA0058.10.0212
MA0059.10.042
MA0060.13.45165e-16
MA0061.10.00189
MA0062.23.21323e-5
MA0065.27.62523e-9
MA0066.10.613
MA0067.10.00313
MA0068.10.623
MA0069.10.752
MA0070.10.279
MA0071.10.334
MA0072.10.375
MA0073.10.725
MA0074.10.679
MA0076.16.96864e-6
MA0077.10.0681
MA0078.10.533
MA0079.20.609
MA0080.23.30875e-9
MA0081.10.149
MA0083.10.0211
MA0084.10.349
MA0087.10.353
MA0088.10.0661
MA0090.10.93
MA0091.10.0693
MA0092.10.0709
MA0093.10.0396
MA0099.27.32719e-10
MA0100.10.0664
MA0101.10.191
MA0102.20.417
MA0103.10.0253
MA0104.20.0111
MA0105.10.00583
MA0106.10.0211
MA0107.10.017
MA0108.20.0543
MA0111.10.786
MA0112.20.906
MA0113.10.995
MA0114.11.15256e-34
MA0115.17.21156e-9
MA0116.10.628
MA0117.10.342
MA0119.10.0381
MA0122.10.306
MA0124.10.435
MA0125.10.349
MA0131.10.203
MA0135.10.261
MA0136.19.11153e-5
MA0137.20.252
MA0138.20.42
MA0139.10.0104
MA0140.10.0172
MA0141.12.80607e-5
MA0142.10.563
MA0143.10.943
MA0144.10.211
MA0145.10.294
MA0146.10.00448
MA0147.10.0155
MA0148.11.893e-4
MA0149.10.254
MA0150.10.00567
MA0152.10.198
MA0153.19.95041e-46
MA0154.10.392
MA0155.10.971
MA0156.10.0119
MA0157.10.271
MA0159.10.165
MA0160.10.00988
MA0162.10.902
MA0163.10.0538
MA0164.10.279
MA0258.10.683
MA0259.10.0775



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: CNhs12329

Novel motifP-value
10.362
100.64
1000.0313
1010.289
1020.168
1030.805
1040.699
1050.822
1060.024
1070.476
1080.509
1090.046
110.901
1100.777
1110.739
1120.228
1130.207
1140.476
1150.984
1160.943
1170.142
1180.182
1190.998
120.653
1200.293
1210.64
1220.924
1230.162
1240.152
1250.603
1260.491
1270.378
1280.0146
1290.846
137.0385e-5
1300.821
1310.0297
1320.473
1330.0102
1340.394
1350.0537
1360.01
1370.00245
1380.436
1390.181
140.063
1400.826
1410.277
1420.755
1430.171
1440.541
1450.726
1460.844
1470.54
1480.746
1490.923
150.759
1500.673
1510.932
1520.807
1530.272
1540.0864
1550.424
1560.862
1570.605
1580.843
1590.771
160.921
1600.789
1610.878
1620.842
1630.727
1640.765
1650.637
1660.309
1670.883
1680.355
1690.271
170.703
180.0909
190.861
20.0991
200.203
210.376
220.441
230.00326
240.903
250.642
260.0552
270.294
280.987
290.16
30.971
300.759
310.673
320.287
330.263
340.468
350.98
360.158
370.921
380.841
390.897
40.846
400.00883
410.0562
420.328
430.897
440.0782
450.963
460.745
470.279
480.502
490.957
50.374
500.179
510.842
520.457
530.186
540.773
550.233
560.829
570.988
580.563
590.734
60.308
600.347
610.106
620.214
630.889
640.947
650.052
660.0106
670.303
680.143
690.364
70.0454
700.11
710.411
720.159
730.0784
740.0596
750.00129
760.7
770.898
780.018
790.0445
80.633
800.0351
810.201
820.0837
830.138
840.115
850.0412
860.637
870.0341
880.473
890.781
90.0732
900.393
910.00927
920.0429
930.751
940.043
950.0013
960.372
970.655
980.781
990.287



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: CNhs12329


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)

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