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FF:10086-102B5: 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 16:54, 29 March 2012


Name:liver, fetal, 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 stage22-40 weeks fetus
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number8101369A-6
catalog numberCat: 636643 Lot: 8101369A-6
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-penis0.178
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-0.00625
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: CNhs11798

Jaspar motifP-value
MA0002.20.647
MA0003.10.0476
MA0004.10.439
MA0006.10.118
MA0007.10.0092
MA0009.10.36
MA0014.10.336
MA0017.12.07006e-20
MA0018.20.506
MA0019.10.468
MA0024.10.819
MA0025.10.314
MA0027.10.988
MA0028.12.27048e-5
MA0029.10.0847
MA0030.10.00835
MA0031.10.0315
MA0035.27.30161e-15
MA0038.10.464
MA0039.20.178
MA0040.10.749
MA0041.10.187
MA0042.10.662
MA0043.10.48
MA0046.11.10993e-86
MA0047.25.65882e-5
MA0048.10.343
MA0050.10.157
MA0051.10.0355
MA0052.10.0763
MA0055.10.958
MA0057.10.449
MA0058.10.442
MA0059.10.348
MA0060.10.075
MA0061.10.26
MA0062.23.35318e-8
MA0065.22.67848e-9
MA0066.10.0402
MA0067.10.14
MA0068.10.299
MA0069.10.469
MA0070.10.25
MA0071.10.0439
MA0072.10.0465
MA0073.10.913
MA0074.10.625
MA0076.12.24788e-6
MA0077.10.713
MA0078.10.82
MA0079.20.455
MA0080.20.0158
MA0081.10.274
MA0083.10.876
MA0084.10.772
MA0087.10.998
MA0088.10.241
MA0090.10.549
MA0091.10.214
MA0092.10.348
MA0093.10.412
MA0099.21.08741e-4
MA0100.10.917
MA0101.10.154
MA0102.20.78
MA0103.10.0437
MA0104.20.823
MA0105.10.651
MA0106.10.722
MA0107.10.0696
MA0108.22.5352e-20
MA0111.10.871
MA0112.26.10911e-4
MA0113.10.101
MA0114.15.11278e-20
MA0115.17.13072e-6
MA0116.10.0359
MA0117.10.601
MA0119.10.58
MA0122.10.502
MA0124.10.946
MA0125.10.208
MA0131.10.469
MA0135.10.217
MA0136.14.38163e-4
MA0137.20.121
MA0138.20.0838
MA0139.10.779
MA0140.11.33827e-18
MA0141.17.25808e-4
MA0142.10.126
MA0143.10.812
MA0144.10.0157
MA0145.10.196
MA0146.10.0143
MA0147.10.981
MA0148.10.00185
MA0149.10.949
MA0150.10.951
MA0152.10.0177
MA0153.11.0556e-41
MA0154.10.1
MA0155.10.0391
MA0156.14.46873e-4
MA0157.10.131
MA0159.10.013
MA0160.10.00818
MA0162.10.258
MA0163.10.293
MA0164.10.488
MA0258.10.00109
MA0259.10.486



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: CNhs11798

Novel motifP-value
10.464
100.879
1000.253
1010.372
1020.209
1030.185
1040.153
1050.303
1060.00347
1070.0209
1080.606
1090.185
110.113
1100.686
1110.962
1120.174
1135.36455e-4
1140.289
1150.628
1160.493
1170.734
1180.401
1190.0983
120.789
1200.499
1210.581
1220.959
1230.312
1240.468
1250.497
1260.199
1270.822
1280.101
1290.559
130.193
1300.0344
1310.42
1320.265
1330.506
1340.515
1350.892
1360.49
1370.336
1380.995
1390.24
140.849
1400.704
1410.0406
1420.231
1430.0633
1440.459
1450.189
1460.339
1470.413
1480.363
1490.238
150.632
1500.748
1510.306
1520.0478
1530.685
1540.364
1550.0473
1560.9
1570.695
1580.729
1590.969
160.272
1600.0134
1610.971
1620.197
1630.437
1640.654
1650.0628
1660.705
1670.757
1680.388
1690.0199
170.355
180.93
190.0126
20.239
200.688
210.255
220.0596
230.114
240.793
250.621
260.307
270.64
280.663
290.712
30.576
300.332
310.303
320.0184
330.56
340.222
350.891
360.359
370.965
380.309
390.278
40.522
400.0064
410.415
420.949
430.152
446.86838e-4
450.0976
460.183
470.544
480.283
490.134
50.575
500.504
510.635
520.0436
530.794
540.402
550.519
560.462
570.81
580.43
590.0463
60.663
600.0203
610.631
620.315
630.479
640.27
650.102
660.605
670.222
680.767
690.155
70.0278
700.0553
710.291
720.668
730.0838
740.163
750.486
760.549
770.0496
780.078
790.957
80.224
800.784
810.978
820.657
830.759
840.276
850.232
860.848
870.656
880.584
890.287
90.479
900.745
910.278
920.214
930.528
940.302
950.557
960.149
970.475
980.736
990.139



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: CNhs11798


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)
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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