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FF:11523-119I2: 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 17:16, 29 March 2012


Name:Hepatocyte, donor1
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 numberNA
catalog numberSC5205
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-penis0.706
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-0.479
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: CNhs12340

Jaspar motifP-value
MA0002.20.793
MA0003.10.0162
MA0004.10.716
MA0006.10.322
MA0007.10.0701
MA0009.10.424
MA0014.10.481
MA0017.17.32059e-20
MA0018.23.65899e-4
MA0019.10.935
MA0024.10.0503
MA0025.10.395
MA0027.10.901
MA0028.10.205
MA0029.10.263
MA0030.10.183
MA0031.10.319
MA0035.20.0241
MA0038.10.135
MA0039.20.493
MA0040.10.671
MA0041.10.766
MA0042.10.727
MA0043.10.0349
MA0046.12.72428e-60
MA0047.27.17142e-4
MA0048.10.995
MA0050.10.967
MA0051.10.968
MA0052.10.0556
MA0055.10.86
MA0057.10.358
MA0058.10.697
MA0059.10.139
MA0060.10.00762
MA0061.10.813
MA0062.20.00687
MA0065.22.17177e-11
MA0066.10.0499
MA0067.10.00371
MA0068.10.00945
MA0069.10.0903
MA0070.10.82
MA0071.10.0777
MA0072.10.0839
MA0073.10.977
MA0074.10.137
MA0076.10.0536
MA0077.10.301
MA0078.10.852
MA0079.20.274
MA0080.25.43536e-8
MA0081.10.0182
MA0083.10.0118
MA0084.10.669
MA0087.10.821
MA0088.10.469
MA0090.10.645
MA0091.10.563
MA0092.10.356
MA0093.10.745
MA0099.23.08867e-7
MA0100.10.44
MA0101.10.0558
MA0102.20.885
MA0103.10.00836
MA0104.20.593
MA0105.10.0365
MA0106.10.359
MA0107.10.0417
MA0108.20.00567
MA0111.10.544
MA0112.21.36333e-6
MA0113.10.13
MA0114.11.39163e-18
MA0115.12.26243e-9
MA0116.11.10544e-4
MA0117.10.697
MA0119.10.0552
MA0122.10.639
MA0124.10.881
MA0125.10.728
MA0131.10.63
MA0135.10.949
MA0136.13.68003e-7
MA0137.20.213
MA0138.20.0707
MA0139.10.108
MA0140.10.0778
MA0141.11.12215e-4
MA0142.10.0286
MA0143.10.248
MA0144.10.113
MA0145.10.586
MA0146.10.207
MA0147.10.472
MA0148.10.00253
MA0149.10.194
MA0150.10.311
MA0152.12.62016e-4
MA0153.11.3779e-35
MA0154.10.0266
MA0155.10.546
MA0156.10.00129
MA0157.10.249
MA0159.19.97319e-5
MA0160.10.00894
MA0162.10.27
MA0163.17.00813e-6
MA0164.10.853
MA0258.11.82311e-4
MA0259.10.768



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: CNhs12340

Novel motifP-value
10.0235
100.119
1000.176
1010.853
1020.209
1030.0436
1040.875
1050.367
1060.0422
1070.0426
1080.338
1090.202
110.172
1100.152
1110.132
1120.0219
1130.266
1140.0213
1150.648
1160.303
1170.238
1180.209
1190.0195
120.463
1200.998
1210.342
1220.579
1230.755
1240.0774
1250.56
1260.105
1270.557
1280.129
1290.0954
130.0748
1300.019
1310.714
1320.583
1330.513
1340.576
1350.847
1360.889
1370.35
1380.281
1390.692
140.674
1400.107
1410.0332
1420.278
1430.037
1440.793
1450.351
1460.123
1470.897
1480.0699
1490.0678
150.125
1500.628
1510.272
1520.643
1530.701
1540.594
1550.0439
1560.695
1570.791
1580.995
1590.744
160.174
1600.135
1610.395
1620.634
1630.654
1640.111
1650.0023
1660.878
1670.0182
1680.745
1693.96185e-4
170.32
180.693
190.0514
20.684
200.735
210.596
220.212
230.26
240.881
250.977
260.0352
270.434
280.75
290.176
30.168
300.875
310.387
320.463
330.4
340.91
350.0815
360.0761
370.249
380.315
390.386
40.497
400.0861
410.398
420.374
430.161
440.00219
450.591
460.106
470.218
480.239
490.161
50.293
500.698
510.733
520.19
530.956
540.556
550.245
560.358
570.484
580.35
590.17
60.703
600.0619
610.617
620.198
630.129
640.317
650.178
660.283
670.0925
680.717
690.872
70.111
700.0808
710.0501
720.495
730.417
740.692
750.131
760.984
770.067
780.0472
790.629
80.0374
800.562
810.298
820.188
830.435
840.397
850.0359
860.41
870.863
880.424
890.0665
90.873
900.129
910.101
920.185
930.427
940.894
950.813
960.171
970.341
980.258
990.124



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: CNhs12340


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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