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FF:11349-117G8: 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 16:47, 29 March 2012


Name:Keratinocyte - epidermal, donor2
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 stage47 years old adult
sexfemale
age47
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 number1331
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-0.182
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-0.235
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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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: CNhs11381

Jaspar motifP-value
MA0002.20.0821
MA0003.10.309
MA0004.10.649
MA0006.10.399
MA0007.10.199
MA0009.10.0302
MA0014.10.676
MA0017.10.116
MA0018.20.0536
MA0019.10.595
MA0024.10.0249
MA0025.10.917
MA0027.10.6
MA0028.10.943
MA0029.10.235
MA0030.10.416
MA0031.10.0929
MA0035.20.117
MA0038.10.816
MA0039.20.0193
MA0040.10.669
MA0041.10.437
MA0042.10.899
MA0043.10.742
MA0046.10.181
MA0047.20.455
MA0048.10.97
MA0050.11.28438e-6
MA0051.11.26033e-4
MA0052.10.927
MA0055.10.174
MA0057.10.0468
MA0058.10.74
MA0059.10.0348
MA0060.10.175
MA0061.10.298
MA0062.20.747
MA0065.20.00458
MA0066.10.00617
MA0067.10.346
MA0068.19.62886e-4
MA0069.10.513
MA0070.10.325
MA0071.10.602
MA0072.10.306
MA0073.10.677
MA0074.10.97
MA0076.10.434
MA0077.10.851
MA0078.10.495
MA0079.20.839
MA0080.20.114
MA0081.10.549
MA0083.10.972
MA0084.10.268
MA0087.10.874
MA0088.10.247
MA0090.10.0428
MA0091.10.689
MA0092.10.303
MA0093.10.699
MA0099.22.90096e-14
MA0100.10.197
MA0101.10.586
MA0102.20.265
MA0103.14.76312e-5
MA0104.20.292
MA0105.10.157
MA0106.15.50562e-7
MA0107.10.478
MA0108.20.00889
MA0111.10.717
MA0112.20.00563
MA0113.10.209
MA0114.10.0495
MA0115.10.525
MA0116.10.0194
MA0117.10.534
MA0119.10.0941
MA0122.10.608
MA0124.10.742
MA0125.10.273
MA0131.10.218
MA0135.10.0931
MA0136.10.701
MA0137.20.0865
MA0138.20.175
MA0139.10.218
MA0140.10.114
MA0141.10.221
MA0142.10.0144
MA0143.10.731
MA0144.10.999
MA0145.10.0702
MA0146.10.0767
MA0147.10.168
MA0148.10.121
MA0149.10.00684
MA0150.10.0884
MA0152.10.238
MA0153.10.178
MA0154.10.0511
MA0155.10.513
MA0156.10.894
MA0157.10.545
MA0159.10.0789
MA0160.10.183
MA0162.10.125
MA0163.10.0267
MA0164.10.601
MA0258.10.0338
MA0259.10.675



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: CNhs11381

Novel motifP-value
10.26
100.706
1000.528
1010.584
1020.466
1030.0815
1040.291
1050.015
1060.0225
1070.0298
1080.422
1090.0103
110.0883
1100.0931
1110.492
1120.34
1130.649
1140.149
1150.925
1160.385
1170.251
1180.714
1190.164
120.457
1200.233
1210.642
1220.156
1230.471
1240.758
1250.29
1260.596
1270.0464
1280.199
1290.183
130.0574
1300.977
1310.334
1320.76
1330.0248
1340.326
1350.609
1360.626
1370.994
1380.284
1390.133
140.847
1400.219
1410.205
1420.116
1430.128
1440.64
1450.124
1460.044
1470.359
1480.906
1490.556
150.19
1500.289
1510.345
1520.0439
1530.612
1540.996
1550.677
1560.299
1570.665
1580.568
1590.74
160.0915
1600.0723
1610.315
1620.134
1630.541
1640.466
1650.985
1660.815
1670.243
1680.397
1690.0461
170.136
180.0316
190.38
20.239
200.93
210.673
220.223
230.244
240.0998
250.948
260.19
270.383
280.693
290.324
30.333
300.349
310.545
320.511
330.246
340.579
350.879
360.322
370.232
380.261
390.304
40.431
400.01
410.657
420.453
430.208
440.666
450.264
460.164
470.219
480.0965
490.273
50.478
500.573
510.611
520.34
531
540.62
550.462
560.26
570.121
580.456
590.0736
60.859
600.0751
610.501
620.451
630.115
640.209
650.148
660.327
670.671
680.828
690.102
70.2
700.00229
710.0795
720.625
730.0339
740.105
750.129
760.919
770.0539
780.197
790.928
80.0896
800.548
810.608
820.368
830.645
840.552
850.128
860.958
870.121
880.214
890.0125
90.656
900.882
910.477
920.417
930.886
940.532
950.0931
960.803
970.927
980.0753
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: CNhs11381


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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