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FF:11422-118F9: 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 17:08, 29 March 2012


Name:Mammary Epithelial Cell, donor3
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 stage30 years old adult
sexfemale
age30
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 number1669
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-penis-0.106
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-lymphoma0.23
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
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs12032

Jaspar motifP-value
MA0002.20.758
MA0003.10.558
MA0004.10.606
MA0006.10.0403
MA0007.10.183
MA0009.10.253
MA0014.10.355
MA0017.10.409
MA0018.25.28235e-4
MA0019.10.42
MA0024.10.328
MA0025.10.569
MA0027.10.229
MA0028.10.166
MA0029.10.175
MA0030.10.578
MA0031.10.105
MA0035.20.355
MA0038.10.0717
MA0039.20.0035
MA0040.10.37
MA0041.10.509
MA0042.10.865
MA0043.10.00335
MA0046.10.685
MA0047.20.776
MA0048.10.34
MA0050.13.74285e-9
MA0051.19.96557e-6
MA0052.10.886
MA0055.10.0109
MA0057.10.0395
MA0058.10.839
MA0059.10.372
MA0060.13.32738e-5
MA0061.10.0891
MA0062.20.0268
MA0065.20.709
MA0066.10.716
MA0067.10.0283
MA0068.10.214
MA0069.10.486
MA0070.10.185
MA0071.10.75
MA0072.10.854
MA0073.10.933
MA0074.10.894
MA0076.10.0183
MA0077.10.02
MA0078.10.25
MA0079.20.242
MA0080.25.60826e-5
MA0081.10.128
MA0083.10.284
MA0084.10.074
MA0087.10.885
MA0088.10.742
MA0090.10.00218
MA0091.10.477
MA0092.10.919
MA0093.10.666
MA0099.28.86984e-7
MA0100.10.604
MA0101.10.199
MA0102.20.0016
MA0103.19.97903e-6
MA0104.20.988
MA0105.10.0829
MA0106.15.34943e-11
MA0107.10.115
MA0108.20.00236
MA0111.10.278
MA0112.20.405
MA0113.10.606
MA0114.10.882
MA0115.10.926
MA0116.10.321
MA0117.10.0475
MA0119.10.238
MA0122.10.72
MA0124.10.84
MA0125.10.529
MA0131.10.429
MA0135.10.0125
MA0136.10.00667
MA0137.20.00734
MA0138.20.219
MA0139.10.841
MA0140.10.528
MA0141.10.798
MA0142.10.0276
MA0143.10.954
MA0144.10.311
MA0145.10.148
MA0146.10.0888
MA0147.10.796
MA0148.10.789
MA0149.10.0488
MA0150.10.808
MA0152.10.669
MA0153.10.192
MA0154.10.974
MA0155.10.476
MA0156.10.0406
MA0157.10.156
MA0159.10.425
MA0160.10.326
MA0162.10.344
MA0163.10.138
MA0164.10.405
MA0258.10.845
MA0259.10.781



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: CNhs12032

Novel motifP-value
10.6
100.0584
1000.919
1010.00626
1020.0982
1030.551
1040.589
1050.301
1060.243
1070.0103
1080.768
1098.51762e-4
110.253
1100.304
1110.626
1120.936
1130.213
1140.849
1150.286
1160.65
1170.369
1180.63
1190.288
120.744
1200.125
1210.407
1220.084
1230.0806
1240.0601
1250.736
1260.604
1270.0628
1280.952
1290.243
130.237
1300.21
1310.475
1320.322
1330.0302
1340.055
1350.884
1360.0515
1370.0135
1380.36
1390.0941
140.882
1400.903
1410.468
1420.0327
1430.996
1440.191
1450.427
1460.00721
1470.246
1480.0564
1490.592
150.639
1500.238
1510.339
1520.0178
1530.396
1540.527
1550.824
1560.577
1570.88
1580.0558
1590.886
160.0764
1600.0863
1610.291
1620.515
1630.852
1640.722
1650.936
1660.63
1670.183
1680.577
1690.195
170.296
180.794
190.983
20.0577
200.764
210.886
220.194
230.956
240.252
250.621
260.289
270.199
280.833
290.891
30.71
300.0193
310.621
320.76
330.244
340.795
350.0633
360.256
370.922
380.448
390.346
40.447
400.0473
410.554
420.783
430.75
440.779
450.0813
460.821
470.466
480.128
490.201
50.271
500.506
510.899
520.479
530.378
540.649
550.649
560.464
570.585
580.437
590.197
60.598
600.413
610.907
620.369
630.327
640.404
650.504
660.228
670.304
680.614
690.0532
70.84
700.782
710.244
720.827
730.00594
740.15
750.791
760.248
770.0323
780.358
790.442
80.314
800.553
810.393
820.706
830.706
840.281
850.831
860.511
870.00401
880.677
890.00482
90.896
900.00161
910.884
920.4
930.365
940.328
950.0273
960.364
970.849
980.47
993.11316e-4



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: CNhs12032


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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