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FF:13366-143F9: 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 17:38, 29 March 2012


Name:HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep3 (UH-3)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexNA
ageNA
cell typeSELECT CELL TYPE
cell lineNA
companyNA
collaborationChristine Mummery/Robert Passier
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberIV-3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-penis0.135
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-lymphoma0.624
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs13738

Jaspar motifP-value
MA0002.21.04136e-4
MA0003.10.0225
MA0004.10.696
MA0006.10.642
MA0007.10.977
MA0009.10.826
MA0014.10.561
MA0017.10.0983
MA0018.20.725
MA0019.10.457
MA0024.12.65553e-8
MA0025.10.156
MA0027.10.421
MA0028.10.174
MA0029.10.383
MA0030.10.0518
MA0031.10.0341
MA0035.20.94
MA0038.10.00522
MA0039.20.0738
MA0040.10.258
MA0041.10.189
MA0042.10.319
MA0043.10.4
MA0046.10.219
MA0047.20.0053
MA0048.10.213
MA0050.12.02751e-10
MA0051.11.82475e-6
MA0052.10.0313
MA0055.10.2
MA0057.10.204
MA0058.10.853
MA0059.10.641
MA0060.11.36805e-14
MA0061.10.00198
MA0062.20.849
MA0065.20.924
MA0066.10.352
MA0067.10.14
MA0068.16.0827e-4
MA0069.10.536
MA0070.10.48
MA0071.10.727
MA0072.10.749
MA0073.10.66
MA0074.10.345
MA0076.10.211
MA0077.10.0308
MA0078.10.391
MA0079.20.818
MA0080.22.89264e-12
MA0081.10.0222
MA0083.10.0145
MA0084.10.351
MA0087.10.29
MA0088.10.909
MA0090.10.273
MA0091.10.0199
MA0092.10.0678
MA0093.10.621
MA0099.21.47646e-21
MA0100.10.549
MA0101.10.0105
MA0102.22.31822e-5
MA0103.10.133
MA0104.20.526
MA0105.10.0171
MA0106.10.894
MA0107.10.00124
MA0108.20.222
MA0111.10.962
MA0112.21.60393e-4
MA0113.10.0032
MA0114.10.89
MA0115.10.468
MA0116.10.0421
MA0117.10.273
MA0119.10.0939
MA0122.10.739
MA0124.10.762
MA0125.10.0142
MA0131.10.492
MA0135.10.0426
MA0136.18.34286e-11
MA0137.20.00817
MA0138.20.511
MA0139.10.629
MA0140.10.623
MA0141.10.458
MA0142.11.59233e-12
MA0143.11.12184e-6
MA0144.10.00329
MA0145.10.174
MA0146.10.165
MA0147.10.514
MA0148.10.0162
MA0149.10.883
MA0150.19.38987e-5
MA0152.10.801
MA0153.10.333
MA0154.10.0174
MA0155.10.764
MA0156.13.85217e-7
MA0157.10.0452
MA0159.10.075
MA0160.10.266
MA0162.10.73
MA0163.19.65072e-4
MA0164.10.972
MA0258.10.0916
MA0259.10.581



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: CNhs13738

Novel motifP-value
10.635
100.212
1000.388
1010.925
1020.836
1030.0632
1040.637
1050.117
1060.0188
1070.53
1080.825
1090.318
110.403
1100.467
1110.197
1120.343
1130.141
1140.0873
1150.749
1160.583
1170.525
1180.989
1190.453
120.725
1200.485
1210.554
1220.477
1230.0597
1240.453
1250.702
1260.304
1270.407
1280.583
1290.635
130.872
1300.903
1310.929
1320.762
1330.129
1340.588
1350.0143
1360.197
1370.223
1380.161
1390.164
140.856
1400.215
1410.955
1420.369
1430.0225
1440.513
1450.844
1460.52
1470.762
1480.0356
1490.0105
150.222
1500.605
1510.0823
1520.0756
1530.181
1540.488
1550.958
1560.426
1570.892
1580.432
1590.737
160.411
1600.353
1610.46
1620.195
1630.162
1640.502
1650.439
1660.733
1670.662
1680.0899
1690.00397
170.179
180.185
190.183
20.226
200.728
210.499
220.0513
230.00385
240.336
250.533
260.946
270.171
280.727
290.555
30.292
300.557
310.894
320.0187
330.935
340.571
350.718
360.557
370.217
380.315
390.422
40.592
400.818
410.0274
420.634
430.137
440.534
450.372
460.301
470.842
480.921
490.201
50.237
500.96
510.33
520.218
530.614
540.238
550.0774
560.665
570.676
580.102
590.0435
60.467
600.0475
610.85
620.0473
630.175
640.645
650.0488
660.487
670.574
680.716
690.469
70.722
700.039
710.0927
720.384
730.0461
740.645
750.24
760.771
770.151
780.708
790.23
80.59
800.0221
810.52
820.148
830.886
840.386
850.0242
860.483
870.383
880.874
890.121
90.0308
900.941
910.692
920.0798
930.135
940.197
950.501
960.179
970.652
980.56
990.562



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: CNhs13738


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)
0000001 (primary cell culture cell)
0000010 (cell culture cell;;obsolete_cell line cell)
0000578 (experimentally modified cell in vitro)

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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