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FF:10065-101I2: 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 16:52, 29 March 2012


Name:skin, fetal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
dev stage26 weeks fetus
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA507299
catalog numberCat:RtHFN: Skin
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-penis-0.0556
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-lymphoma0.043
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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: CNhs11774

Jaspar motifP-value
MA0002.27.16818e-5
MA0003.10.999
MA0004.10.00628
MA0006.10.577
MA0007.10.0713
MA0009.10.259
MA0014.10.201
MA0017.10.119
MA0018.20.063
MA0019.10.783
MA0024.10.879
MA0025.10.0122
MA0027.10.475
MA0028.11.10923e-6
MA0029.10.285
MA0030.10.882
MA0031.10.512
MA0035.20.125
MA0038.10.684
MA0039.20.414
MA0040.10.545
MA0041.10.583
MA0042.10.719
MA0043.10.00886
MA0046.10.107
MA0047.20.6
MA0048.10.103
MA0050.18.58037e-4
MA0051.10.00507
MA0052.14.8915e-13
MA0055.10.019
MA0057.10.818
MA0058.16.12061e-4
MA0059.10.00105
MA0060.10.142
MA0061.17.62777e-8
MA0062.21.08599e-13
MA0065.20.036
MA0066.10.12
MA0067.10.00897
MA0068.13.5306e-4
MA0069.10.866
MA0070.10.428
MA0071.10.491
MA0072.10.23
MA0073.10.566
MA0074.10.304
MA0076.17.46567e-8
MA0077.10.752
MA0078.10.422
MA0079.20.431
MA0080.23.97192e-8
MA0081.10.0052
MA0083.10.2
MA0084.10.0298
MA0087.10.0883
MA0088.10.0356
MA0090.10.0519
MA0091.10.281
MA0092.10.724
MA0093.10.00685
MA0099.22.50557e-24
MA0100.10.205
MA0101.18.68351e-7
MA0102.20.0525
MA0103.10.935
MA0104.21.69086e-4
MA0105.14.46982e-9
MA0106.10.135
MA0107.11.35805e-6
MA0108.24.68908e-23
MA0111.10.595
MA0112.20.596
MA0113.10.451
MA0114.10.0332
MA0115.10.0922
MA0116.11.18645e-4
MA0117.10.146
MA0119.10.72
MA0122.10.634
MA0124.10.667
MA0125.10.365
MA0131.10.455
MA0135.10.37
MA0136.13.49468e-13
MA0137.20.859
MA0138.20.0428
MA0139.10.00871
MA0140.10.022
MA0141.10.051
MA0142.10.0432
MA0143.10.413
MA0144.10.644
MA0145.10.359
MA0146.10.239
MA0147.18.41587e-5
MA0148.10.786
MA0149.10.0743
MA0150.18.50829e-13
MA0152.10.022
MA0153.10.663
MA0154.10.015
MA0155.10.177
MA0156.13.10573e-14
MA0157.10.304
MA0159.10.114
MA0160.10.00512
MA0162.10.7
MA0163.10.0027
MA0164.10.504
MA0258.10.825
MA0259.10.0308



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: CNhs11774

Novel motifP-value
10.0893
100.116
1000.485
1010.917
1020.348
1030.0738
1040.781
1050.84
1060.906
1070.235
1080.454
1090.00175
110.0858
1100.266
1110.153
1120.714
1130.00362
1140.0398
1150.0425
1160.801
1170.00496
1180.0201
1190.644
120.383
1200.664
1210.851
1220.0393
1230.837
1240.328
1250.347
1260.79
1270.209
1280.847
1290.904
130.299
1300.99
1310.911
1320.0351
1330.302
1340.506
1350.737
1360.17
1370.498
1380.485
1390.238
140.47
1400.479
1410.517
1420.735
1430.00189
1440.991
1450.603
1460.528
1470.238
1480.292
1490.696
150.0693
1500.413
1510.899
1520.732
1530.391
1540.538
1550.379
1560.296
1570.456
1580.0414
1590.771
160.651
1600.867
1610.393
1620.0611
1630.29
1640.109
1650.481
1660.0269
1670.0348
1680.673
1690.304
170.487
180.0374
190.398
20.0949
200.0337
210.811
220.582
230.48
240.0782
250.472
260.432
270.619
280.841
290.0246
30.259
300.0259
310.892
326.96111e-8
330.21
340.434
350.316
360.036
370.041
380.536
390.133
40.592
400.0519
410.0896
420.219
430.177
440.841
450.553
460.314
470.136
480.26
490.129
50.416
500.612
510.567
520.378
530.579
540.987
550.423
560.489
570.927
580.481
590.83
60.623
600.893
610.0599
620.535
630.78
640.297
650.956
660.0314
670.165
680.672
690.956
70.504
700.23
710.053
720.523
730.0589
740.302
750.00768
760.0252
770.677
780.896
790.979
80.336
800.262
810.924
820.504
830.683
840.697
850.764
860.27
870.00325
880.665
890.833
90.875
900.097
910.139
920.896
930.614
940.075
950.00531
960.508
970.956
980.226
990.07



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: CNhs11774


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
0000014 (zone of skin)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001003 (skin epidermis)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002097 (skin of body)
0002199 (integument)
0002416 (integumental system)
0002532 (epiblast (generic))
0003102 (surface structure)
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)
0007029 (surface)
0007376 (outer epithelium)
0007383 (enveloping layer of ectoderm)

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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