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FF:10018-101C9: 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 16:26, 29 March 2012


Name:liver, adult, pool1
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 stage64,69,70 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0910061 -9
catalog numberCat:AM6000 Lot:0910061 -9
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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-penis0.0738
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-0.453
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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: CNhs10624

Jaspar motifP-value
MA0002.20.452
MA0003.10.00866
MA0004.10.586
MA0006.10.112
MA0007.10.0247
MA0009.10.326
MA0014.10.579
MA0017.17.6359e-27
MA0018.20.0103
MA0019.10.246
MA0024.10.0128
MA0025.10.331
MA0027.10.723
MA0028.10.104
MA0029.10.357
MA0030.13.63931e-4
MA0031.10.00213
MA0035.21.76772e-4
MA0038.10.735
MA0039.20.414
MA0040.10.218
MA0041.10.113
MA0042.10.547
MA0043.10.541
MA0046.17.40142e-92
MA0047.22.46454e-8
MA0048.10.331
MA0050.10.543
MA0051.10.231
MA0052.10.715
MA0055.10.553
MA0057.10.0914
MA0058.10.365
MA0059.10.131
MA0060.10.0124
MA0061.10.412
MA0062.20.00799
MA0065.22.52696e-14
MA0066.10.0613
MA0067.10.0337
MA0068.10.201
MA0069.10.337
MA0070.10.278
MA0071.10.0389
MA0072.10.0132
MA0073.10.588
MA0074.10.0956
MA0076.10.0481
MA0077.10.337
MA0078.10.677
MA0079.20.356
MA0080.20.0307
MA0081.10.259
MA0083.10.605
MA0084.10.785
MA0087.10.284
MA0088.10.68
MA0090.10.695
MA0091.10.782
MA0092.10.239
MA0093.10.51
MA0099.27.11106e-8
MA0100.10.24
MA0101.10.0532
MA0102.20.393
MA0103.10.00495
MA0104.20.987
MA0105.10.792
MA0106.10.889
MA0107.10.0758
MA0108.20.108
MA0111.10.826
MA0112.23.08069e-6
MA0113.10.0939
MA0114.13.14159e-25
MA0115.19.48278e-11
MA0116.10.00888
MA0117.10.746
MA0119.10.21
MA0122.10.454
MA0124.10.787
MA0125.10.521
MA0131.10.233
MA0135.10.47
MA0136.10.018
MA0137.23.12049e-5
MA0138.20.064
MA0139.10.266
MA0140.10.139
MA0141.11.63627e-6
MA0142.10.0851
MA0143.10.383
MA0144.16.12565e-4
MA0145.10.144
MA0146.10.125
MA0147.10.967
MA0148.12.36461e-5
MA0149.10.531
MA0150.10.591
MA0152.17.1364e-5
MA0153.13.46492e-46
MA0154.10.084
MA0155.10.107
MA0156.10.183
MA0157.10.0183
MA0159.14.28532e-5
MA0160.12.03708e-4
MA0162.10.325
MA0163.10.134
MA0164.10.444
MA0258.10.00242
MA0259.10.315



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: CNhs10624

Novel motifP-value
10.212
100.721
1000.506
1010.674
1020.202
1030.0523
1040.659
1050.969
1060.0121
1070.0122
1080.483
1090.176
110.243
1100.338
1110.593
1120.0179
1130.499
1140.129
1150.526
1160.363
1170.918
1180.49
1190.0767
120.579
1200.862
1210.304
1220.757
1230.0299
1240.2
1250.197
1260.173
1270.679
1280.142
1290.216
130.119
1300.27
1310.914
1320.381
1330.23
1340.956
1350.212
1360.828
1370.364
1380.768
1390.873
140.879
1400.655
1410.17
1420.499
1430.145
1440.389
1450.309
1460.0175
1470.948
1480.0902
1490.0279
150.306
1500.53
1510.382
1520.0568
1530.825
1540.169
1550.0555
1560.972
1570.403
1580.483
1590.979
160.217
1600.286
1610.98
1620.401
1630.807
1640.814
1650.0164
1660.854
1670.799
1680.476
1690.0034
170.295
180.73
190.016
20.19
200.831
210.0921
220.0737
230.159
240.524
250.897
260.156
270.315
280.909
290.572
30.453
300.256
310.301
320.339
330.338
340.311
350.37
360.369
370.3
380.325
390.113
40.139
400.0571
410.328
420.629
430.197
445.13928e-4
450.176
460.308
470.476
480.34
490.307
50.242
500.507
510.69
520.0857
530.713
540.47
550.776
560.61
570.702
580.325
590.054
60.176
600.0507
610.435
620.264
630.204
640.618
650.14
660.195
670.135
680.772
690.801
70.0935
700.426
710.181
720.151
730.104
740.986
750.559
760.336
770.00975
780.147
790.895
80.0751
800.48
810.695
820.266
830.803
840.334
850.0455
860.343
870.336
880.542
890.0765
90.581
900.653
910.388
920.196
930.446
940.26
950.572
960.236
970.29
980.91
990.0955



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: CNhs10624


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

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)
0007023 (adult organism)
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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