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FF:11355-117H5: 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:Placental Epithelial Cells, donor2
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
sexfemale
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 number2544
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-0.188
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-lymphoma0.0182
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
C115-pituitary-Neural-caudate-putamen-amygdala-medulla-hippocampus0
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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: CNhs11386

Jaspar motifP-value
MA0002.20.745
MA0003.10.221
MA0004.10.681
MA0006.10.109
MA0007.10.00265
MA0009.10.382
MA0014.10.556
MA0017.10.766
MA0018.20.00508
MA0019.10.0913
MA0024.10.325
MA0025.10.55
MA0027.10.813
MA0028.10.266
MA0029.10.359
MA0030.10.282
MA0031.10.2
MA0035.20.657
MA0038.10.238
MA0039.20.124
MA0040.10.543
MA0041.10.491
MA0042.10.738
MA0043.10.00195
MA0046.10.571
MA0047.20.915
MA0048.10.729
MA0050.13.64259e-8
MA0051.16.30029e-5
MA0052.10.872
MA0055.10.0687
MA0057.10.624
MA0058.10.746
MA0059.10.267
MA0060.10.274
MA0061.10.93
MA0062.20.00305
MA0065.20.0762
MA0066.10.181
MA0067.10.0254
MA0068.10.0357
MA0069.10.728
MA0070.10.187
MA0071.10.294
MA0072.10.447
MA0073.10.442
MA0074.10.519
MA0076.10.0519
MA0077.10.492
MA0078.10.536
MA0079.20.642
MA0080.21.06908e-8
MA0081.10.00892
MA0083.10.465
MA0084.10.856
MA0087.10.471
MA0088.10.416
MA0090.12.1633e-4
MA0091.10.13
MA0092.10.333
MA0093.10.702
MA0099.29.8035e-5
MA0100.10.134
MA0101.10.0643
MA0102.20.00148
MA0103.10.0128
MA0104.20.611
MA0105.10.346
MA0106.10.0754
MA0107.10.0428
MA0108.20.0164
MA0111.10.921
MA0112.20.00308
MA0113.16.6057e-4
MA0114.10.238
MA0115.10.667
MA0116.10.0439
MA0117.10.58
MA0119.10.28
MA0122.10.729
MA0124.10.474
MA0125.10.89
MA0131.10.252
MA0135.10.743
MA0136.11.81404e-8
MA0137.20.0489
MA0138.20.207
MA0139.10.571
MA0140.10.796
MA0141.10.314
MA0142.10.387
MA0143.10.549
MA0144.10.866
MA0145.10.153
MA0146.10.0361
MA0147.10.905
MA0148.10.988
MA0149.10.5
MA0150.10.953
MA0152.10.811
MA0153.10.355
MA0154.10.0824
MA0155.10.165
MA0156.13.30076e-7
MA0157.10.247
MA0159.10.209
MA0160.10.488
MA0162.10.0557
MA0163.10.0213
MA0164.10.74
MA0258.10.0134
MA0259.10.795



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: CNhs11386

Novel motifP-value
10.489
100.799
1000.327
1010.861
1020.508
1030.135
1040.606
1050.279
1060.0677
1070.079
1080.55
1090.0108
110.11
1100.099
1110.903
1120.623
1130.151
1140.351
1150.848
1160.326
1170.423
1180.257
1190.182
120.809
1200.12
1210.566
1220.173
1230.319
1240.951
1250.816
1260.532
1270.502
1280.674
1290.184
130.176
1300.0776
1310.476
1320.869
1330.102
1340.349
1350.507
1360.372
1370.323
1380.0578
1390.464
140.685
1400.879
1410.422
1420.573
1430.406
1440.815
1450.734
1460.0636
1470.141
1480.9
1490.0641
150.325
1500.381
1510.461
1520.0587
1530.541
1540.588
1550.305
1560.544
1570.465
1580.917
1590.539
160.0319
1600.0172
1610.186
1620.0561
1630.532
1640.318
1650.772
1660.588
1670.204
1680.356
1690.0662
170.0412
180.0966
190.163
20.215
200.994
210.817
220.0787
230.23
240.805
250.977
260.131
270.326
280.7
290.209
30.706
300.186
310.419
327.49436e-9
330.169
340.44
350.744
360.489
370.168
380.374
390.0899
40.196
400.0056
410.607
420.965
430.236
440.606
450.231
460.272
470.433
480.109
490.26
50.713
500.553
510.259
520.431
530.841
540.431
550.984
560.327
570.361
580.854
590.0526
60.953
600.399
610.867
620.921
630.334
640.155
650.234
660.274
670.0803
680.342
697.42423e-4
70.398
700.231
710.127
720.794
730.0489
740.179
750.203
760.411
770.0201
780.453
790.184
80.181
800.866
810.763
820.351
830.967
840.414
850.355
860.706
870.37
880.412
890.147
90.488
900.162
910.0557
920.994
930.966
940.365
950.185
960.856
970.242
980.434
990.0192



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: CNhs11386


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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