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FF:11427-118G5: 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:Placental Epithelial Cells, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueplacenta
dev stageNA
sexunknown
ageNA
cell typeplacental 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 number2637
catalog numberCA230-R10f
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-0.0942
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-lymphoma0.119
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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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: CNhs12037

Jaspar motifP-value
MA0002.20.0944
MA0003.10.339
MA0004.10.944
MA0006.10.0993
MA0007.10.0205
MA0009.10.611
MA0014.10.589
MA0017.10.735
MA0018.20.0146
MA0019.10.0381
MA0024.10.13
MA0025.10.706
MA0027.10.402
MA0028.10.932
MA0029.10.197
MA0030.10.0951
MA0031.10.0686
MA0035.20.961
MA0038.10.00942
MA0039.20.0595
MA0040.10.701
MA0041.10.538
MA0042.10.784
MA0043.10.00664
MA0046.10.808
MA0047.20.352
MA0048.10.501
MA0050.17.24438e-8
MA0051.12.17634e-6
MA0052.10.781
MA0055.10.00467
MA0057.10.521
MA0058.10.636
MA0059.10.883
MA0060.19.90304e-5
MA0061.10.172
MA0062.20.0378
MA0065.20.219
MA0066.10.396
MA0067.10.00777
MA0068.10.985
MA0069.10.741
MA0070.10.0266
MA0071.10.871
MA0072.10.778
MA0073.10.631
MA0074.10.441
MA0076.10.347
MA0077.10.681
MA0078.10.867
MA0079.20.261
MA0080.26.89737e-10
MA0081.10.00488
MA0083.10.492
MA0084.10.966
MA0087.10.473
MA0088.10.953
MA0090.12.68668e-4
MA0091.10.271
MA0092.10.565
MA0093.10.889
MA0099.20.266
MA0100.10.213
MA0101.10.0147
MA0102.20.0162
MA0103.10.175
MA0104.20.254
MA0105.10.613
MA0106.10.113
MA0107.10.0104
MA0108.27.28833e-7
MA0111.10.574
MA0112.20.129
MA0113.10.0072
MA0114.10.824
MA0115.10.306
MA0116.10.569
MA0117.10.349
MA0119.10.974
MA0122.10.91
MA0124.10.902
MA0125.10.452
MA0131.10.426
MA0135.10.109
MA0136.11.92015e-9
MA0137.20.203
MA0138.20.248
MA0139.10.993
MA0140.10.419
MA0141.10.724
MA0142.10.577
MA0143.10.788
MA0144.10.957
MA0145.10.272
MA0146.10.019
MA0147.10.314
MA0148.10.371
MA0149.10.613
MA0150.10.0335
MA0152.10.81
MA0153.10.525
MA0154.10.391
MA0155.10.12
MA0156.18.78822e-6
MA0157.10.022
MA0159.10.558
MA0160.10.554
MA0162.10.0666
MA0163.10.252
MA0164.10.544
MA0258.10.487
MA0259.10.412



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: CNhs12037

Novel motifP-value
10.208
100.3
1000.238
1010.108
1020.509
1030.908
1040.931
1050.531
1060.181
1070.251
1080.396
1090.0214
110.605
1100.222
1110.391
1120.689
1130.0836
1140.585
1150.0794
1160.182
1170.536
1180.395
1190.939
120.794
1200.0871
1210.232
1220.507
1230.00447
1240.0755
1250.247
1260.428
1270.979
1280.988
1290.689
130.27
1300.0898
1310.0294
1320.437
1330.377
1340.121
1350.93
1360.0478
1370.0185
1380.171
1390.168
140.808
1400.557
1410.984
1420.259
1430.633
1440.887
1450.836
1460.233
1470.302
1480.0123
1490.274
150.314
1500.263
1510.429
1520.0463
1530.0442
1540.254
1550.304
1560.285
1570.594
1580.528
1590.723
160.0973
1600.0751
1610.0936
1620.27
1630.895
1640.368
1650.711
1660.802
1670.12
1680.79
1690.0891
170.188
180.787
190.288
20.0739
200.847
210.925
220.0736
230.858
240.711
250.559
260.42
270.558
280.474
290.304
30.621
300.063
310.481
325.65071e-9
330.362
340.359
350.16
360.278
370.589
380.898
390.318
40.747
400.00839
410.341
420.357
430.951
440.558
450.183
460.902
470.834
480.548
490.342
50.152
500.491
510.461
520.547
530.284
540.575
550.373
560.527
570.764
580.259
590.0592
60.739
600.994
610.782
620.153
630.991
640.351
650.499
660.531
670.732
680.787
690.0147
70.989
700.518
710.602
720.728
730.028
740.0292
750.604
760.159
770.00495
780.938
790.0113
80.97
800.78
810.19
820.885
830.843
840.287
850.986
860.622
870.159
880.276
890.0996
90.338
900.0166
910.586
920.247
930.764
940.557
950.0961
960.218
970.484
980.823
990.0161



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: CNhs12037


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)
0000349 (extraembryonic cell)
0000548 (animal cell)
0002371 (somatic cell)
0002577 (placental epithelial cell)

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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