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FF:11278-116H9: 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 16:39, 29 March 2012


Name:Placental Epithelial Cells, donor1
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 stagefetus
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 number2628
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-0.22
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-lymphoma-0.0972
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: CNhs11079

Jaspar motifP-value
MA0002.20.244
MA0003.10.466
MA0004.10.0523
MA0006.10.118
MA0007.10.0263
MA0009.10.653
MA0014.10.302
MA0017.10.7
MA0018.20.0103
MA0019.10.00104
MA0024.10.14
MA0025.10.285
MA0027.10.806
MA0028.11.89992e-6
MA0029.10.178
MA0030.10.191
MA0031.10.0786
MA0035.20.0353
MA0038.15.55625e-4
MA0039.20.00494
MA0040.10.921
MA0041.10.405
MA0042.10.716
MA0043.10.747
MA0046.10.326
MA0047.20.813
MA0048.10.536
MA0050.14.24999e-10
MA0051.16.39631e-6
MA0052.10.329
MA0055.12.80064e-5
MA0057.10.77
MA0058.10.0189
MA0059.10.219
MA0060.11.06498e-7
MA0061.10.948
MA0062.22.52653e-7
MA0065.20.0698
MA0066.10.206
MA0067.10.727
MA0068.10.875
MA0069.10.918
MA0070.10.0312
MA0071.10.828
MA0072.10.0675
MA0073.10.697
MA0074.10.481
MA0076.11.15119e-7
MA0077.10.92
MA0078.10.782
MA0079.20.32
MA0080.23.63497e-8
MA0081.10.272
MA0083.10.595
MA0084.10.383
MA0087.10.724
MA0088.10.17
MA0090.10.00105
MA0091.10.799
MA0092.10.39
MA0093.10.0589
MA0099.22.21451e-10
MA0100.10.284
MA0101.10.285
MA0102.20.00125
MA0103.10.00143
MA0104.20.702
MA0105.10.773
MA0106.10.0607
MA0107.10.237
MA0108.25.35537e-15
MA0111.10.822
MA0112.20.175
MA0113.10.0254
MA0114.10.285
MA0115.10.621
MA0116.10.641
MA0117.10.654
MA0119.10.787
MA0122.10.592
MA0124.10.143
MA0125.10.0985
MA0131.10.914
MA0135.10.14
MA0136.10.0452
MA0137.20.513
MA0138.20.603
MA0139.10.983
MA0140.10.835
MA0141.10.395
MA0142.10.902
MA0143.10.26
MA0144.10.963
MA0145.10.215
MA0146.10.0253
MA0147.10.533
MA0148.10.763
MA0149.10.386
MA0150.10.652
MA0152.10.931
MA0153.10.503
MA0154.10.389
MA0155.10.403
MA0156.10.484
MA0157.10.0472
MA0159.10.171
MA0160.10.179
MA0162.10.0955
MA0163.10.0946
MA0164.10.295
MA0258.10.64
MA0259.10.697



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: CNhs11079

Novel motifP-value
10.828
100.886
1000.145
1010.0839
1020.127
1030.397
1040.48
1050.109
1060.228
1070.909
1080.807
1094.62919e-5
110.437
1100.119
1110.572
1120.847
1130.775
1140.665
1150.428
1160.31
1170.0501
1180.13
1190.396
120.465
1200.128
1210.158
1220.00235
1230.0128
1240.21
1250.68
1260.445
1270.756
1280.552
1290.292
130.00778
1300.23
1310.148
1320.964
1330.139
1340.17
1350.568
1360.012
1370.062
1380.0962
1390.565
140.892
1400.912
1410.506
1420.162
1430.818
1440.967
1450.877
1460.26
1470.709
1480.00769
1490.552
150.86
1500.297
1510.482
1520.0315
1530.0355
1540.235
1550.0655
1560.0149
1570.281
1580.656
1590.964
160.245
1600.15
1610.0679
1620.901
1630.767
1640.312
1650.702
1660.114
1670.432
1680.963
1690.0805
170.169
180.834
190.743
20.251
200.113
210.569
220.0774
230.198
240.264
250.736
260.272
270.405
280.94
290.0243
30.877
300.091
310.476
320.542
330.0857
340.849
350.16
360.448
370.128
380.463
390.242
40.511
406.82331e-4
410.769
420.943
430.738
440.97
450.141
460.897
470.542
480.218
490.893
50.415
500.365
510.561
520.72
530.27
540.961
550.49
560.723
570.625
580.575
590.133
60.898
600.699
610.389
620.299
630.824
640.406
650.644
660.0315
670.328
680.306
690.0073
70.244
700.79
710.64
720.533
730.0039
740.0241
750.0985
760.938
770.0634
780.117
790.853
80.974
800.819
810.123
820.857
830.826
840.366
850.997
860.884
870.017
880.372
890.0917
90.719
900.155
910.463
920.0896
930.987
940.993
950.00153
960.678
970.442
980.912
990.0946



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: CNhs11079


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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