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FF:11251-116E9: 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 16:36, 29 March 2012


Name:Keratinocyte - oral, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuegum
dev stageNA
sexunknown
ageNA
cell typekeratinocyte
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:4853
catalog numberSciencell(2615)
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-0.115
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-lymphoma0.187
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs10879

Jaspar motifP-value
MA0002.20.0139
MA0003.10.899
MA0004.10.197
MA0006.10.15
MA0007.10.924
MA0009.10.271
MA0014.10.392
MA0017.10.751
MA0018.26.5816e-5
MA0019.10.915
MA0024.10.361
MA0025.10.331
MA0027.10.413
MA0028.10.405
MA0029.10.399
MA0030.10.169
MA0031.10.345
MA0035.20.584
MA0038.10.583
MA0039.20.0022
MA0040.10.0467
MA0041.10.619
MA0042.10.483
MA0043.10.0468
MA0046.10.752
MA0047.20.657
MA0048.10.842
MA0050.14.25605e-7
MA0051.10.00178
MA0052.10.029
MA0055.10.0213
MA0057.10.265
MA0058.10.0218
MA0059.10.938
MA0060.10.727
MA0061.10.603
MA0062.20.0949
MA0065.20.221
MA0066.10.271
MA0067.10.00491
MA0068.10.00731
MA0069.10.161
MA0070.10.887
MA0071.10.101
MA0072.10.114
MA0073.10.716
MA0074.10.663
MA0076.10.488
MA0077.10.659
MA0078.10.859
MA0079.20.319
MA0080.25.64225e-6
MA0081.10.0281
MA0083.10.0802
MA0084.10.351
MA0087.10.797
MA0088.10.296
MA0090.10.00148
MA0091.10.1
MA0092.10.43
MA0093.10.125
MA0099.23.58414e-4
MA0100.10.943
MA0101.10.13
MA0102.20.445
MA0103.13.66438e-7
MA0104.20.68
MA0105.10.629
MA0106.14.35335e-13
MA0107.10.091
MA0108.20.0817
MA0111.10.435
MA0112.20.725
MA0113.10.683
MA0114.10.224
MA0115.10.47
MA0116.10.423
MA0117.10.274
MA0119.10.295
MA0122.10.857
MA0124.10.693
MA0125.10.0299
MA0131.10.388
MA0135.10.284
MA0136.10.00455
MA0137.20.179
MA0138.20.153
MA0139.10.702
MA0140.10.263
MA0141.10.236
MA0142.10.22
MA0143.10.243
MA0144.10.834
MA0145.10.0492
MA0146.10.186
MA0147.10.493
MA0148.10.18
MA0149.10.26
MA0150.10.0783
MA0152.10.988
MA0153.10.984
MA0154.10.448
MA0155.10.738
MA0156.10.0148
MA0157.10.165
MA0159.10.663
MA0160.10.0877
MA0162.10.355
MA0163.10.796
MA0164.10.992
MA0258.10.222
MA0259.10.866



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: CNhs10879

Novel motifP-value
10.837
100.58
1000.938
1010.445
1020.197
1030.115
1040.905
1050.0495
1060.959
1070.0384
1080.735
1090.00478
110.487
1100.18
1110.358
1120.874
1130.815
1140.717
1150.603
1160.419
1170.329
1180.528
1190.981
120.792
1200.00202
1210.819
1220.397
1230.162
1240.207
1250.675
1260.339
1270.602
1280.982
1290.0573
130.0247
1300.341
1310.443
1320.0926
1335.39545e-4
1340.0751
1350.789
1360.0121
1370.144
1380.941
1390.0503
140.919
1400.49
1410.45
1420.226
1430.325
1440.407
1450.252
1460.0288
1470.369
1480.0798
1490.673
150.199
1500.532
1510.578
1520.212
1530.382
1540.515
1550.942
1560.957
1570.987
1580.133
1590.361
160.111
1600.0506
1610.231
1620.14
1630.806
1640.883
1650.911
1660.446
1670.16
1680.461
1690.194
170.221
180.916
190.605
20.0829
200.936
210.937
220.479
230.7
240.00153
250.949
260.745
270.62
280.608
290.339
30.539
300.0454
310.997
320.105
330.0914
340.728
350.125
360.45
370.832
380.418
390.255
40.84
400.159
410.115
420.489
430.948
440.405
450.0444
460.788
470.398
480.173
490.22
50.467
500.351
510.675
520.544
530.435
540.979
550.653
560.481
570.438
580.825
590.556
60.122
600.809
610.934
620.724
630.335
640.626
650.738
660.423
670.316
680.129
690.743
70.51
700.2
710.904
720.527
730.153
740.0293
750.242
760.782
770.0414
780.0335
790.248
80.512
800.106
810.322
820.786
830.276
840.637
850.747
860.259
870.21
880.572
890.267
90.753
900.925
910.989
920.707
930.882
940.831
950.146
960.328
970.867
980.75
990.0382



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: CNhs10879


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)
0000223 (endodermal cell)
0000237 (keratinizing barrier epithelial cell)
0000240 (stratified squamous epithelial cell)
0000255 (eukaryotic cell)
0000311 (keratin accumulating cell)
0000325 (stuff accumulating cell)
0000357 (stratified epithelial stem cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002076 (endo-epithelial cell)
0002170 (keratinized cell of the oral mucosa)
0002261 (endothelial cell of viscerocranial mucosa)
0002321 (embryonic cell)
0002336 (buccal mucosa cell)
0002371 (somatic cell)

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000153 (anterior region of body)
0000165 (mouth)
0000344 (mucosa)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000930 (stomodeum)
0001007 (digestive system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003729 (mouth mucosa)
0004119 (endoderm-derived structure)
0004923 (organ component layer)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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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