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FF:11350-117G9: 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 16:48, 29 March 2012


Name:Mammary Epithelial Cell, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebreast
dev stage28 years old adult
sexfemale
age28
cell typemammary gland epithelial cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2049
catalog numberCA830-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-penis0.106
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-lymphoma0.478
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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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: CNhs11382

Jaspar motifP-value
MA0002.20.354
MA0003.10.461
MA0004.10.273
MA0006.10.0869
MA0007.10.381
MA0009.10.13
MA0014.10.0975
MA0017.10.891
MA0018.20.0078
MA0019.10.914
MA0024.10.00191
MA0025.10.514
MA0027.10.853
MA0028.18.47295e-4
MA0029.10.462
MA0030.10.223
MA0031.10.248
MA0035.20.232
MA0038.10.543
MA0039.20.00102
MA0040.10.35
MA0041.10.724
MA0042.10.806
MA0043.10.304
MA0046.10.642
MA0047.20.389
MA0048.10.433
MA0050.11.16476e-8
MA0051.13.68107e-5
MA0052.10.0125
MA0055.10.00514
MA0057.10.00714
MA0058.10.019
MA0059.10.46
MA0060.10.26
MA0061.10.248
MA0062.20.0215
MA0065.20.277
MA0066.10.643
MA0067.10.0163
MA0068.19.64734e-4
MA0069.10.22
MA0070.10.601
MA0071.10.402
MA0072.10.805
MA0073.10.789
MA0074.10.616
MA0076.10.0265
MA0077.10.61
MA0078.10.599
MA0079.20.776
MA0080.25.82392e-5
MA0081.10.521
MA0083.10.044
MA0084.10.28
MA0087.10.296
MA0088.10.261
MA0090.10.00571
MA0091.10.154
MA0092.10.401
MA0093.10.186
MA0099.25.5783e-6
MA0100.10.325
MA0101.10.278
MA0102.20.0686
MA0103.12.45449e-6
MA0104.20.259
MA0105.10.797
MA0106.14.53596e-20
MA0107.10.103
MA0108.20.00215
MA0111.10.85
MA0112.20.646
MA0113.10.938
MA0114.10.607
MA0115.10.973
MA0116.10.527
MA0117.10.409
MA0119.10.347
MA0122.10.669
MA0124.10.563
MA0125.10.0577
MA0131.10.157
MA0135.10.287
MA0136.10.2
MA0137.20.131
MA0138.20.585
MA0139.10.447
MA0140.10.459
MA0141.10.326
MA0142.10.0761
MA0143.10.302
MA0144.10.756
MA0145.10.105
MA0146.10.52
MA0147.10.143
MA0148.10.286
MA0149.10.0233
MA0150.10.818
MA0152.10.507
MA0153.10.694
MA0154.10.945
MA0155.10.0623
MA0156.10.459
MA0157.10.0477
MA0159.10.653
MA0160.10.685
MA0162.10.572
MA0163.10.553
MA0164.10.837
MA0258.10.225
MA0259.10.221



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: CNhs11382

Novel motifP-value
10.455
100.884
1000.591
1010.195
1020.194
1030.0699
1040.868
1050.709
1060.547
1070.245
1080.722
1092.78611e-4
110.73
1100.23
1110.0359
1120.834
1130.0281
1140.545
1150.846
1160.352
1170.927
1180.555
1190.476
120.703
1200.0182
1210.972
1220.223
1230.345
1240.056
1250.429
1260.403
1270.059
1280.285
1290.14
130.0406
1300.89
1310.272
1320.162
1330.0171
1340.236
1350.756
1360.0163
1370.264
1380.204
1390.0775
140.608
1400.822
1410.225
1420.507
1430.512
1440.0424
1450.999
1460.305
1470.222
1480.409
1490.243
150.915
1500.453
1510.455
1520.137
1530.738
1540.73
1550.82
1560.586
1570.531
1580.0439
1590.519
160.00388
1600.472
1610.874
1620.501
1630.221
1640.492
1650.114
1660.0678
1670.81
1680.284
1690.0933
170.521
180.321
190.744
20.447
200.714
210.805
220.839
230.897
240.0031
250.501
260.956
270.747
280.312
290.228
30.951
300.0534
310.94
320.17
330.0618
340.181
350.0569
360.563
370.482
380.401
390.495
40.888
400.244
410.582
420.61
430.67
440.464
450.587
460.995
470.376
480.09
490.366
50.614
500.301
511
520.887
530.189
540.928
550.567
560.498
570.375
580.876
590.86
60.75
600.457
610.414
620.517
630.194
640.971
650.976
660.0811
670.938
680.314
690.375
70.451
700.677
710.149
720.976
730.00836
740.552
750.133
760.834
770.619
780.146
790.0977
80.655
800.878
810.857
820.503
830.442
840.0802
850.137
860.331
870.00462
880.867
890.0196
90.264
900.685
910.933
920.356
930.596
940.492
950.00395
960.736
970.455
980.736
990.0405



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: CNhs11382


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)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002327 (mammary gland epithelial cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000076 (external ectoderm)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001048 (primordium)
0001062 (anatomical entity)
0001911 (mammary gland)
0002050 (embryonic structure)
0002330 (exocrine system)
0002365 (exocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0003100 (female organism)
0004121 (ectoderm-derived structure)
0005085 (ectodermal placode)
0005153 (epithelial bud)
0005291 (embryonic tissue)
0005311 (mammary placode)
0005333 (mammary bud)
0005423 (developing anatomical structure)
0008425 (mammary ridge)

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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