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FF:11603-120I1: 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 17:17, 29 March 2012


Name:Hepatocyte, donor2
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-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-penis0.381
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-0.452
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12349

Jaspar motifP-value
MA0002.20.444
MA0003.10.0103
MA0004.10.554
MA0006.10.254
MA0007.10.0627
MA0009.10.786
MA0014.10.307
MA0017.12.96656e-15
MA0018.21.63658e-4
MA0019.10.945
MA0024.10.013
MA0025.10.564
MA0027.10.968
MA0028.10.0934
MA0029.10.363
MA0030.10.216
MA0031.10.102
MA0035.20.0239
MA0038.10.107
MA0039.20.629
MA0040.10.374
MA0041.10.336
MA0042.10.676
MA0043.10.0144
MA0046.11.23756e-61
MA0047.23.19839e-5
MA0048.10.817
MA0050.10.875
MA0051.10.824
MA0052.10.52
MA0055.10.788
MA0057.10.171
MA0058.10.453
MA0059.10.0628
MA0060.12.18495e-5
MA0061.10.876
MA0062.20.0014
MA0065.23.12633e-9
MA0066.10.0283
MA0067.10.0131
MA0068.10.0399
MA0069.10.296
MA0070.10.382
MA0071.10.0512
MA0072.10.0838
MA0073.10.646
MA0074.10.261
MA0076.10.0214
MA0077.10.431
MA0078.10.804
MA0079.20.413
MA0080.22.89897e-4
MA0081.10.122
MA0083.10.0788
MA0084.10.608
MA0087.10.69
MA0088.10.371
MA0090.10.764
MA0091.10.882
MA0092.10.407
MA0093.10.548
MA0099.24.5346e-6
MA0100.10.374
MA0101.10.217
MA0102.20.745
MA0103.10.0043
MA0104.20.448
MA0105.10.154
MA0106.10.297
MA0107.10.203
MA0108.20.276
MA0111.10.745
MA0112.24.53556e-7
MA0113.10.219
MA0114.12.64876e-13
MA0115.13.05902e-7
MA0116.14.88315e-4
MA0117.10.645
MA0119.10.0473
MA0122.10.722
MA0124.10.853
MA0125.10.855
MA0131.10.306
MA0135.10.855
MA0136.11.65999e-5
MA0137.20.00711
MA0138.20.0317
MA0139.10.144
MA0140.10.0866
MA0141.14.92118e-5
MA0142.10.00717
MA0143.10.103
MA0144.10.00749
MA0145.10.306
MA0146.10.0583
MA0147.10.351
MA0148.16.53285e-4
MA0149.10.197
MA0150.10.691
MA0152.14.31821e-5
MA0153.11.63567e-42
MA0154.10.0159
MA0155.10.343
MA0156.10.0149
MA0157.10.0529
MA0159.14.5834e-4
MA0160.10.0122
MA0162.10.357
MA0163.14.41973e-4
MA0164.10.666
MA0258.15.04605e-4
MA0259.10.79



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: CNhs12349

Novel motifP-value
10.0426
100.204
1000.228
1010.998
1020.265
1030.147
1040.77
1050.377
1060.00558
1070.0172
1080.392
1090.185
110.167
1100.237
1110.179
1120.0119
1130.229
1140.023
1150.726
1160.237
1170.36
1180.375
1190.0182
120.503
1200.96
1210.159
1220.527
1230.764
1240.0444
1250.298
1260.218
1270.72
1280.0493
1290.202
130.106
1300.0686
1310.857
1320.447
1330.688
1340.737
1350.393
1360.748
1370.765
1380.201
1390.316
140.8
1400.221
1410.0697
1420.202
1430.359
1440.749
1450.129
1460.161
1470.655
1480.0244
1490.0612
150.0987
1500.479
1510.204
1520.258
1530.818
1540.537
1550.0602
1560.942
1570.892
1580.883
1590.43
160.256
1600.208
1610.627
1620.41
1630.72
1640.244
1650.0301
1660.808
1670.111
1680.742
1694.91825e-4
170.232
180.243
190.0732
20.529
200.998
210.627
220.132
230.109
240.873
250.948
260.0285
270.42
280.866
290.42
30.219
300.948
310.352
320.399
330.346
340.568
350.0824
360.0536
370.216
380.277
390.329
40.301
400.0712
410.34
420.541
430.123
441.71914e-5
450.474
460.0997
470.332
480.262
490.123
50.225
500.458
510.618
520.105
530.963
540.377
550.706
560.621
570.486
580.339
590.0898
60.789
600.0368
610.412
620.177
630.111
640.432
650.0964
660.463
670.237
680.644
690.533
70.113
700.0767
710.0665
720.595
730.164
740.819
750.133
760.943
770.0536
780.0707
790.336
80.0478
800.673
810.256
820.166
830.608
840.301
850.0203
860.272
870.924
880.509
890.0869
90.964
900.0628
910.184
920.103
930.417
940.841
950.616
960.189
970.57
980.403
990.0548



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: CNhs12349


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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