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FF:11272-116H3: 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 16:38, 29 March 2012


Name:Keratinocyte - epidermal, 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 stage54 years old adult
sexmale
age54
cell typekeratinocyte
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1327
catalog numberCA102-R10a
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-0.0895
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-0.181
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs11064

Jaspar motifP-value
MA0002.20.933
MA0003.10.708
MA0004.10.52
MA0006.10.0427
MA0007.10.744
MA0009.10.0243
MA0014.10.291
MA0017.10.794
MA0018.25.72441e-4
MA0019.10.381
MA0024.11.42887e-6
MA0025.10.383
MA0027.10.555
MA0028.10.626
MA0029.10.189
MA0030.10.162
MA0031.10.0317
MA0035.20.431
MA0038.10.102
MA0039.20.00247
MA0040.10.433
MA0041.10.497
MA0042.10.663
MA0043.10.0208
MA0046.10.753
MA0047.20.842
MA0048.10.776
MA0050.11.99341e-8
MA0051.11.25826e-5
MA0052.10.0375
MA0055.10.535
MA0057.10.0127
MA0058.10.269
MA0059.10.562
MA0060.10.0477
MA0061.10.544
MA0062.20.126
MA0065.20.144
MA0066.10.368
MA0067.10.00186
MA0068.10.0127
MA0069.10.16
MA0070.10.748
MA0071.10.148
MA0072.10.748
MA0073.10.848
MA0074.10.777
MA0076.10.314
MA0077.10.191
MA0078.10.701
MA0079.20.188
MA0080.28.34245e-7
MA0081.10.0222
MA0083.10.0108
MA0084.10.109
MA0087.10.97
MA0088.10.447
MA0090.13.96739e-4
MA0091.10.486
MA0092.10.869
MA0093.10.437
MA0099.21.12484e-5
MA0100.10.103
MA0101.10.2
MA0102.20.00321
MA0103.12.59665e-6
MA0104.20.703
MA0105.10.95
MA0106.17.90293e-11
MA0107.10.18
MA0108.20.483
MA0111.10.854
MA0112.20.154
MA0113.10.845
MA0114.10.592
MA0115.10.764
MA0116.10.158
MA0117.10.386
MA0119.10.37
MA0122.10.562
MA0124.10.964
MA0125.10.0764
MA0131.10.184
MA0135.10.584
MA0136.14.38173e-4
MA0137.20.0246
MA0138.20.562
MA0139.10.546
MA0140.10.535
MA0141.10.481
MA0142.10.358
MA0143.10.282
MA0144.10.842
MA0145.10.0146
MA0146.10.201
MA0147.10.97
MA0148.10.563
MA0149.10.162
MA0150.10.813
MA0152.10.383
MA0153.10.51
MA0154.10.198
MA0155.10.875
MA0156.10.0103
MA0157.10.0714
MA0159.10.506
MA0160.10.339
MA0162.10.101
MA0163.10.916
MA0164.10.396
MA0258.10.971
MA0259.10.788



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: CNhs11064

Novel motifP-value
10.828
100.206
1000.867
1010.308
1020.27
1030.0573
1040.916
1050.208
1060.0492
1070.0479
1080.204
1090.0137
110.474
1100.383
1110.617
1120.163
1130.275
1140.341
1150.224
1160.969
1170.371
1180.954
1190.455
120.652
1200.079
1210.953
1220.203
1230.114
1240.0952
1250.838
1260.31
1270.139
1280.341
1290.0858
130.141
1300.861
1310.763
1320.302
1330.00839
1340.167
1350.988
1360.0946
1370.191
1380.538
1390.606
140.752
1400.749
1410.686
1420.395
1430.856
1440.232
1450.121
1460.0895
1470.0823
1480.721
1490.452
150.807
1500.248
1510.234
1520.0142
1530.57
1540.897
1550.986
1560.811
1570.671
1580.0383
1590.46
160.0308
1600.281
1610.344
1620.512
1630.685
1640.849
1650.772
1660.321
1670.0973
1680.123
1690.0457
170.256
180.144
190.953
20.0983
200.803
210.754
220.417
230.406
240.00718
250.753
260.516
270.437
280.755
290.62
30.505
300.0557
310.716
320.866
330.396
340.899
350.356
360.0839
370.25
380.62
390.102
40.892
400.0641
410.413
420.84
430.626
440.137
450.0765
460.683
470.543
480.187
490.703
50.967
500.478
510.686
520.181
530.513
540.479
550.251
560.394
570.577
580.988
590.151
60.157
600.347
610.903
620.787
630.202
640.826
650.707
660.583
670.924
680.24
690.0627
70.503
700.0541
710.482
720.563
730.00825
740.0504
750.431
760.38
770.00403
780.0718
790.651
80.349
800.873
810.793
820.427
830.96
840.618
850.51
860.908
870.0198
880.868
890.00568
90.965
900.596
910.571
920.484
930.964
940.744
950.087
960.987
970.799
980.758
990.0023



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: CNhs11064


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)
0000035 (single fate stem cell)
0000036 (epithelial fate stem cell)
0000066 (epithelial cell)
0000076 (squamous epithelial cell)
0000079 (stratified epithelial cell)
0000114 (surface ectodermal cell)
0000221 (ectodermal cell)
0000237 (keratinizing barrier epithelial cell)
0000240 (stratified squamous epithelial cell)
0000255 (eukaryotic cell)
0000311 (keratin accumulating cell)
0000312 (keratinocyte)
0000325 (stuff accumulating cell)
0000357 (stratified epithelial stem cell)
0000362 (epidermal cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002077 (ecto-epithelial cell)
0002159 (general ecto-epithelial cell)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
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)
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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