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FF:11255-116F4: 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 16:34, 29 March 2012


Name:Sertoli Cells, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuetestis
dev stage23 years old adult
sexmale
age23
cell typesertoli cell
cell lineNA
companyLonza
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-0.117
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-lymphoma0.155
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: CNhs10851

Jaspar motifP-value
MA0002.20.568
MA0003.10.423
MA0004.10.109
MA0006.10.469
MA0007.10.157
MA0009.10.401
MA0014.10.314
MA0017.10.303
MA0018.21.53121e-6
MA0019.10.397
MA0024.12.2918e-4
MA0025.10.0793
MA0027.10.987
MA0028.16.00347e-4
MA0029.10.85
MA0030.10.279
MA0031.10.293
MA0035.20.656
MA0038.10.00619
MA0039.20.0457
MA0040.10.371
MA0041.10.421
MA0042.10.979
MA0043.10.00324
MA0046.10.811
MA0047.20.444
MA0048.10.906
MA0050.10.422
MA0051.10.928
MA0052.10.429
MA0055.10.255
MA0057.10.194
MA0058.10.0125
MA0059.10.888
MA0060.11.98668e-9
MA0061.10.627
MA0062.24.46511e-10
MA0065.20.198
MA0066.10.194
MA0067.10.001
MA0068.10.325
MA0069.10.353
MA0070.10.653
MA0071.10.532
MA0072.10.638
MA0073.10.632
MA0074.10.474
MA0076.14.41584e-5
MA0077.10.83
MA0078.10.517
MA0079.20.471
MA0080.21.36181e-7
MA0081.10.00348
MA0083.10.0248
MA0084.10.694
MA0087.10.778
MA0088.10.789
MA0090.11.20374e-7
MA0091.10.00779
MA0092.10.0059
MA0093.10.0658
MA0099.20.371
MA0100.10.287
MA0101.10.26
MA0102.20.295
MA0103.10.747
MA0104.20.11
MA0105.10.0299
MA0106.10.00605
MA0107.10.385
MA0108.20.0117
MA0111.10.557
MA0112.26.43814e-5
MA0113.10.15
MA0114.10.772
MA0115.10.592
MA0116.10.0153
MA0117.10.994
MA0119.10.0363
MA0122.10.0759
MA0124.10.615
MA0125.10.491
MA0131.10.434
MA0135.10.0298
MA0136.12.98373e-9
MA0137.20.443
MA0138.20.515
MA0139.10.905
MA0140.10.757
MA0141.10.357
MA0142.10.579
MA0143.10.12
MA0144.10.772
MA0145.10.125
MA0146.10.808
MA0147.10.606
MA0148.10.697
MA0149.10.149
MA0150.10.609
MA0152.10.00585
MA0153.10.324
MA0154.10.0173
MA0155.10.376
MA0156.19.91965e-6
MA0157.10.714
MA0159.10.166
MA0160.10.924
MA0162.10.0457
MA0163.16.27336e-5
MA0164.10.594
MA0258.10.00506
MA0259.10.843



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: CNhs10851

Novel motifP-value
10.124
100.638
1000.696
1010.735
1020.126
1030.082
1040.791
1050.806
1060.0231
1070.0267
1080.373
1090.157
110.285
1100.246
1110.973
1120.468
1130.194
1140.0927
1150.368
1160.0719
1170.739
1180.972
1190.263
120.362
1200.901
1210.817
1220.504
1230.158
1240.532
1250.768
1260.983
1270.895
1280.0476
1290.385
130.677
1300.384
1310.0723
1320.716
1330.789
1340.12
1350.146
1360.508
1370.653
1380.581
1390.566
140.866
1400.442
1410.539
1420.584
1430.048
1440.705
1450.362
1460.584
1470.183
1480.445
1491.6355e-4
150.175
1500.383
1510.415
1520.122
1530.158
1540.86
1550.216
1560.46
1570.888
1580.0771
1590.411
160.026
1600.141
1610.245
1620.83
1630.514
1640.212
1650.992
1660.0733
1670.566
1680.859
1690.0339
170.22
180.0435
190.0356
20.144
200.327
210.148
220.191
230.0204
240.673
250.798
260.0933
270.158
280.436
290.723
30.251
300.402
310.521
321.0594e-11
330.435
340.604
350.214
360.401
370.211
380.83
390.213
40.949
400.749
410.407
420.513
430.302
440.681
450.433
460.0637
470.443
480.471
490.297
50.307
500.534
510.916
520.132
530.871
540.532
550.0934
560.782
570.269
580.789
590.0752
60.643
600.112
610.521
620.192
630.179
640.557
650.227
660.99
670.123
680.974
690.445
70.921
700.104
710.0742
720.714
730.251
740.00924
750.325
760.755
770.00838
780.532
790.0112
80.0467
800.754
810.27
820.24
830.4
840.975
850.0355
860.519
870.797
880.456
890.046
90.387
900.171
910.53
920.124
930.516
940.152
950.452
960.318
970.171
980.888
990.00427



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: CNhs10851


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)
0000066 (epithelial cell)
0000076 (squamous epithelial cell)
0000077 (mesothelial cell)
0000151 (secretory cell)
0000154 (protein secreting cell)
0000213 (lining cell)
0000215 (barrier cell)
0000216 (Sertoli cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000511 (androgen binding protein secreting cell)
0000548 (animal cell)
0000630 (supportive cell)
0002321 (embryonic cell)
0002625 (seminiferous tubule epithelial cell)

UBERON: Anatomy
0000058 (duct)
0000061 (anatomical structure)
0000062 (organ)
0000079 (male reproductive system)
0000119 (cell layer)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000473 (testis)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000487 (simple squamous epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000991 (gonad)
0001048 (primordium)
0001062 (anatomical entity)
0001136 (mesothelium)
0001343 (seminiferous tubule of testis)
0002050 (embryonic structure)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003101 (male organism)
0003133 (reproductive organ)
0003135 (male reproductive organ)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004176 (external genitalia)
0004458 (body cavity or lining)
0004813 (seminiferous tubule epithelium)
0004909 (epithelium of gonad)
0004910 (epithelium of male gonad)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005564 (gonad primordium)
0005904 (duct of male reproductive system)
0006914 (squamous epithelium)
0009117 (indifferent gonad)
0009196 (indifferent external genitalia)

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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