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FF:11273-116H4: 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:Mammary Epithelial Cell, donor1
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 stage29 years old adult
sexfemale
age29
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 number1691
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-penis0.28
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-lymphoma0.428
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
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: CNhs11077

Jaspar motifP-value
MA0002.20.055
MA0003.10.208
MA0004.10.423
MA0006.10.247
MA0007.10.458
MA0009.10.367
MA0014.10.088
MA0017.10.387
MA0018.20.105
MA0019.10.744
MA0024.10.00401
MA0025.10.933
MA0027.10.581
MA0028.11.2108e-5
MA0029.10.71
MA0030.10.203
MA0031.10.331
MA0035.20.0135
MA0038.10.635
MA0039.20.00452
MA0040.10.0354
MA0041.10.306
MA0042.10.106
MA0043.10.839
MA0046.10.435
MA0047.20.572
MA0048.10.138
MA0050.17.57905e-8
MA0051.15.03906e-6
MA0052.18.71642e-4
MA0055.10.00155
MA0057.10.159
MA0058.10.0505
MA0059.10.538
MA0060.10.241
MA0061.10.17
MA0062.21.92435e-4
MA0065.20.869
MA0066.10.644
MA0067.10.101
MA0068.10.041
MA0069.10.215
MA0070.10.703
MA0071.10.0791
MA0072.10.509
MA0073.10.997
MA0074.10.656
MA0076.16.5206e-5
MA0077.10.954
MA0078.10.637
MA0079.20.515
MA0080.28.11824e-6
MA0081.10.198
MA0083.10.0023
MA0084.10.415
MA0087.10.111
MA0088.10.527
MA0090.14.59118e-4
MA0091.10.023
MA0092.10.305
MA0093.10.255
MA0099.24.721e-5
MA0100.10.0969
MA0101.10.323
MA0102.20.332
MA0103.18.20804e-5
MA0104.20.505
MA0105.10.715
MA0106.12.20236e-16
MA0107.10.0561
MA0108.21.07343e-6
MA0111.10.828
MA0112.20.888
MA0113.10.453
MA0114.10.86
MA0115.10.928
MA0116.10.468
MA0117.10.73
MA0119.10.361
MA0122.10.363
MA0124.10.499
MA0125.10.418
MA0131.10.0754
MA0135.10.607
MA0136.10.0328
MA0137.20.0259
MA0138.20.867
MA0139.10.522
MA0140.10.0784
MA0141.10.11
MA0142.10.214
MA0143.10.782
MA0144.10.682
MA0145.10.0699
MA0146.10.721
MA0147.10.252
MA0148.10.283
MA0149.10.0587
MA0150.10.69
MA0152.10.12
MA0153.10.24
MA0154.10.436
MA0155.10.00795
MA0156.10.538
MA0157.10.0683
MA0159.10.943
MA0160.10.131
MA0162.10.99
MA0163.10.203
MA0164.10.681
MA0258.10.0688
MA0259.10.183



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: CNhs11077

Novel motifP-value
10.733
100.689
1000.593
1010.177
1020.303
1030.199
1040.69
1050.993
1060.437
1070.311
1080.834
1090.00965
110.904
1100.177
1110.131
1120.846
1130.0487
1140.908
1150.73
1160.645
1170.356
1180.811
1190.45
120.422
1200.0509
1210.432
1220.506
1230.397
1240.0155
1250.374
1260.624
1270.456
1280.134
1290.405
130.0418
1300.668
1310.19
1320.269
1330.139
1340.209
1350.171
1360.0104
1370.0958
1380.446
1390.0842
140.438
1400.77
1410.188
1420.263
1430.389
1440.152
1450.897
1460.415
1470.663
1480.218
1490.227
150.891
1500.262
1510.922
1520.21
1530.252
1540.747
1550.913
1560.632
1570.349
1580.0446
1590.358
160.0508
1600.907
1610.981
1620.45
1630.371
1640.0945
1650.0762
1660.356
1670.987
1680.543
1690.337
170.349
180.521
190.566
20.881
200.0727
210.574
220.627
230.887
240.0121
250.675
260.973
270.209
280.122
290.489
30.787
300.307
310.643
320.124
330.0396
340.0284
350.053
360.602
370.527
380.968
390.484
40.462
400.66
410.135
420.673
430.588
440.894
450.698
460.594
470.599
480.189
490.21
50.561
500.315
510.385
520.753
530.138
540.72
550.321
560.906
570.24
580.825
590.257
60.978
600.653
610.621
620.517
630.352
640.694
650.255
660.139
670.946
680.135
690.657
70.949
700.0893
710.45
720.904
730.0326
740.872
750.0889
760.385
770.758
780.0428
790.109
80.763
800.367
810.214
820.16
830.798
840.374
850.151
860.513
870.0345
880.711
890.0601
90.137
900.106
910.62
920.153
930.995
940.701
950.013
960.755
970.847
980.369
990.325



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: CNhs11077


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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