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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000015,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002100,UBERON:0002107,UBERON:0002330,UBERON:0002365,UBERON:0002368,UBERON:0002405,UBERON:0002417,UBERON:0002423,UBERON:0002530,UBERON:0002532,UBERON:0003104,UBERON:0003894,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004921,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0006235,UBERON:0006925,UBERON:0007026,UBERON:0008835,UBERON:0008836,UBERON:0009142
|ancestors_in_anatomy_facet=UBERON:0000015,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002100,UBERON:0002107,UBERON:0002330,UBERON:0002365,UBERON:0002368,UBERON:0002405,UBERON:0002417,UBERON:0002423,UBERON:0002530,UBERON:0002532,UBERON:0003104,UBERON:0003894,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004921,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0006235,UBERON:0006925,UBERON:0007026,UBERON:0008835,UBERON:0008836,UBERON:0009142
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100224,FF:0101120
|fonse_cell_line=FF:0100224,FF:0101120
|fonse_cell_line_closure=FF:0100224,FF:0101120
|fonse_cell_line_closure=FF:0100224,FF:0101120

Revision as of 16:42, 29 March 2012


Name:hepatoma cell line:Li-7
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueliver
dev stageNA
sexmale
age45
cell typehepatocyte
cell lineLi-7
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
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-lymphoma0.168
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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 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: CNhs11271

Jaspar motifP-value
MA0002.20.00251
MA0003.10.468
MA0004.10.237
MA0006.10.921
MA0007.10.119
MA0009.10.895
MA0014.10.823
MA0017.10.0242
MA0018.20.207
MA0019.10.497
MA0024.10.021
MA0025.10.776
MA0027.10.881
MA0028.10.114
MA0029.10.698
MA0030.10.0428
MA0031.19.21611e-4
MA0035.20.154
MA0038.10.136
MA0039.20.00703
MA0040.10.82
MA0041.10.616
MA0042.10.469
MA0043.10.119
MA0046.11.43665e-85
MA0047.23.94401e-8
MA0048.10.263
MA0050.10.867
MA0051.10.698
MA0052.10.00804
MA0055.10.183
MA0057.10.347
MA0058.10.448
MA0059.10.806
MA0060.10.00252
MA0061.10.00286
MA0062.20.858
MA0065.20.044
MA0066.10.154
MA0067.10.473
MA0068.10.353
MA0069.10.226
MA0070.10.457
MA0071.10.822
MA0072.10.398
MA0073.10.255
MA0074.10.352
MA0076.10.129
MA0077.10.0472
MA0078.10.531
MA0079.20.0939
MA0080.21.86567e-9
MA0081.10.0173
MA0083.10.635
MA0084.10.871
MA0087.10.606
MA0088.10.884
MA0090.10.687
MA0091.10.191
MA0092.10.251
MA0093.10.228
MA0099.20.0612
MA0100.10.297
MA0101.10.28
MA0102.20.0805
MA0103.10.0262
MA0104.20.23
MA0105.12.4317e-4
MA0106.10.215
MA0107.10.0639
MA0108.20.398
MA0111.10.396
MA0112.20.0962
MA0113.10.0892
MA0114.16.8577e-6
MA0115.10.0606
MA0116.19.12658e-4
MA0117.10.126
MA0119.10.493
MA0122.10.69
MA0124.10.365
MA0125.10.00482
MA0131.10.318
MA0135.10.167
MA0136.13.42038e-7
MA0137.20.577
MA0138.20.00646
MA0139.10.0738
MA0140.10.159
MA0141.10.867
MA0142.10.0786
MA0143.10.634
MA0144.10.645
MA0145.10.299
MA0146.10.138
MA0147.10.491
MA0148.13.67732e-6
MA0149.10.974
MA0150.10.331
MA0152.10.693
MA0153.13.41215e-62
MA0154.10.0676
MA0155.10.762
MA0156.16.00061e-5
MA0157.10.0768
MA0159.10.12
MA0160.10.743
MA0162.10.532
MA0163.10.00613
MA0164.10.51
MA0258.10.158
MA0259.10.751



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: CNhs11271

Novel motifP-value
10.564
100.55
1000.0805
1010.131
1020.0628
1030.34
1040.513
1050.662
1060.922
1070.418
1080.564
1090.0711
110.0121
1100.156
1110.477
1120.375
1136.95257e-4
1140.234
1150.598
1160.246
1170.118
1180.278
1190.965
120.172
1200.721
1210.0354
1220.706
1230.831
1240.304
1250.846
1260.411
1270.0141
1280.00547
1290.605
130.45
1300.897
1310.242
1320.271
1330.479
1340.53
1350.179
1360.0825
1370.195
1380.879
1390.513
140.512
1400.313
1410.149
1420.89
1431.42638e-4
1440.769
1450.514
1460.573
1470.223
1480.346
1490.605
150.493
1500.839
1510.608
1520.809
1530.111
1540.41
1550.542
1560.389
1570.305
1580.256
1590.836
160.286
1600.055
1610.849
1620.973
1630.21
1640.921
1650.749
1660.348
1670.36
1680.4
1690.0865
170.389
180.407
190.199
20.19
200.029
210.485
220.0657
230.379
240.697
250.435
260.532
270.0165
280.687
290.332
30.14
300.357
310.964
322.80139e-4
330.603
340.333
350.899
360.628
370.247
380.457
390.652
40.336
400.708
410.00385
420.353
430.123
440.974
450.832
460.476
470.418
480.214
490.32
50.476
500.977
510.0874
520.916
530.451
540.83
550.362
560.817
570.75
580.305
590.0798
60.565
600.71
610.975
620.0585
630.784
640.436
650.172
660.138
670.0162
680.172
690.757
70.304
700.397
710.161
720.277
730.621
740.579
750.819
760.727
770.568
780.128
790.00296
80.67
800.294
810.573
820.0117
830.384
840.579
850.271
860.445
870.434
880.973
890.112
90.00778
900.927
910.107
920.534
930.939
940.0834
950.324
960.326
970.867
980.247
990.626



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: CNhs11271


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

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

UBERON: Anatomy
0000015 (anatomical boundary)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
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)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003894 (liver primordium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0007026 (primitive gut)
0008835 (hepatic diverticulum)
0008836 (liver bud)
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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