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FF:11684-122I1: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:23, 29 March 2012


Name:Hepatocyte, donor3
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
sexNA
ageNA
cell typehepatocyte
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNA1057
catalog numberSC5205
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-penis0.758
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-lymphoma-0.372
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 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: CNhs12626

Jaspar motifP-value
MA0002.20.42
MA0003.10.0224
MA0004.10.797
MA0006.10.248
MA0007.10.00597
MA0009.10.413
MA0014.10.626
MA0017.13.0979e-25
MA0018.20.0177
MA0019.10.792
MA0024.10.0168
MA0025.10.741
MA0027.10.776
MA0028.10.00341
MA0029.10.756
MA0030.10.0161
MA0031.10.0607
MA0035.20.014
MA0038.10.497
MA0039.20.482
MA0040.10.62
MA0041.10.894
MA0042.10.751
MA0043.10.355
MA0046.11.327e-69
MA0047.24.63124e-5
MA0048.10.619
MA0050.10.859
MA0051.10.955
MA0052.10.858
MA0055.10.642
MA0057.10.196
MA0058.10.759
MA0059.10.46
MA0060.10.0262
MA0061.10.0116
MA0062.21.62359e-6
MA0065.28.17741e-13
MA0066.10.568
MA0067.10.0191
MA0068.10.0567
MA0069.10.207
MA0070.10.446
MA0071.10.265
MA0072.10.139
MA0073.10.895
MA0074.10.402
MA0076.11.72196e-4
MA0077.10.418
MA0078.10.775
MA0079.20.943
MA0080.23.25646e-5
MA0081.10.0277
MA0083.10.149
MA0084.10.903
MA0087.10.342
MA0088.10.362
MA0090.10.876
MA0091.10.911
MA0092.10.525
MA0093.10.776
MA0099.25.93952e-18
MA0100.10.154
MA0101.16.46738e-4
MA0102.20.286
MA0103.10.0599
MA0104.20.573
MA0105.10.0597
MA0106.10.71
MA0107.15.05165e-4
MA0108.20.0657
MA0111.10.867
MA0112.24.22876e-5
MA0113.10.0588
MA0114.11.22125e-28
MA0115.14.20168e-8
MA0116.10.00543
MA0117.10.457
MA0119.10.0514
MA0122.10.861
MA0124.10.98
MA0125.10.397
MA0131.10.334
MA0135.10.846
MA0136.11.15362e-4
MA0137.20.00135
MA0138.20.0654
MA0139.10.809
MA0140.10.564
MA0141.12.24522e-4
MA0142.10.199
MA0143.10.311
MA0144.10.00273
MA0145.10.362
MA0146.10.424
MA0147.10.798
MA0148.10.00266
MA0149.10.801
MA0150.10.0874
MA0152.16.06755e-4
MA0153.11.30752e-36
MA0154.10.287
MA0155.10.204
MA0156.15.53798e-4
MA0157.10.379
MA0159.11.91505e-4
MA0160.10.0147
MA0162.10.919
MA0163.10.311
MA0164.10.472
MA0258.10.00162
MA0259.10.323



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: CNhs12626

Novel motifP-value
10.171
100.82
1000.246
1010.905
1020.0634
1030.319
1040.505
1050.43
1060.00392
1070.00587
1080.251
1090.902
110.403
1100.577
1110.307
1120.0129
1132.31647e-4
1140.15
1150.854
1160.35
1170.275
1180.314
1190.0079
120.57
1200.688
1210.903
1220.221
1230.796
1240.0803
1250.118
1260.553
1270.0896
1280.16
1290.727
130.0898
1300.0127
1310.981
1320.0556
1330.319
1340.775
1350.525
1360.0894
1370.299
1380.29
1390.962
140.631
1400.537
1410.136
1420.273
1430.00249
1440.445
1450.265
1460.47
1470.948
1480.175
1490.146
151
1500.891
1510.451
1520.949
1530.816
1540.406
1550.0485
1560.708
1570.469
1580.311
1590.0708
160.603
1600.503
1610.973
1620.589
1630.598
1640.378
1650.00189
1660.283
1670.492
1680.63
1690.001
170.447
180.639
190.00157
20.185
200.98
210.12
220.0783
230.0518
240.76
250.802
260.251
270.514
280.946
290.94
30.528
300.646
310.22
320.406
330.995
340.254
350.299
360.391
370.982
380.227
390.238
40.156
400.258
410.0829
420.977
430.253
440.00459
450.332
460.254
470.818
480.488
490.151
50.285
500.399
510.937
520.0419
530.846
540.509
550.829
560.891
570.968
580.253
590.215
60.619
600.0222
610.662
620.211
630.15
640.659
650.0753
660.0539
670.0742
680.936
690.99
70.101
700.98
710.265
720.662
730.962
740.888
750.565
760.329
770.0271
780.175
790.829
80.137
800.984
810.721
820.307
830.972
840.45
850.00756
860.763
870.0394
880.318
890.278
90.842
900.511
910.175
920.344
930.586
940.194
950.14
960.0451
970.92
980.957
990.0694



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: CNhs12626


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000066 (epithelial cell)
0000134 (mesenchymal cell)
0000181 (metabolising cell)
0000182 (hepatocyte)
0000219 (motile cell)
0000223 (endodermal cell)
0000255 (eukaryotic cell)
0000412 (polyploid cell)
0000417 (endopolyploid cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002321 (embryonic cell)
0002371 (somatic cell)

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)
0002384 (connective tissue)
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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