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FF:12822-136I5: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100669
|fonse_cell_line=FF:0100669
|fonse_cell_line_closure=FF:0100669
|fonse_cell_line_closure=FF:0100669

Revision as of 17:25, 29 March 2012


Name:H9 Embryonic Stem cells, biol_rep3 (H9ES-3)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueunclassifiable
dev stageNA
sexfemale
ageNA
cell typestem cell
cell lineH9
companyNA
collaborationSusan Zabierowski (Wistar Institute)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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
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-lymphoma0.625
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
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: CNhs12837

Jaspar motifP-value
MA0002.20.00141
MA0003.10.102
MA0004.10.488
MA0006.10.655
MA0007.10.732
MA0009.10.442
MA0014.10.427
MA0017.10.223
MA0018.20.455
MA0019.10.445
MA0024.13.95351e-6
MA0025.10.349
MA0027.10.503
MA0028.10.0919
MA0029.10.615
MA0030.10.687
MA0031.10.398
MA0035.20.596
MA0038.15.45714e-4
MA0039.20.0419
MA0040.10.913
MA0041.10.858
MA0042.10.801
MA0043.10.813
MA0046.10.621
MA0047.20.109
MA0048.10.668
MA0050.15.65272e-8
MA0051.12.36268e-4
MA0052.10.145
MA0055.10.123
MA0057.10.382
MA0058.10.425
MA0059.10.779
MA0060.11.4231e-15
MA0061.10.0162
MA0062.20.535
MA0065.20.624
MA0066.10.31
MA0067.10.142
MA0068.10.0309
MA0069.10.251
MA0070.10.0127
MA0071.10.99
MA0072.10.799
MA0073.10.889
MA0074.10.583
MA0076.10.0686
MA0077.10.0488
MA0078.10.48
MA0079.20.132
MA0080.21.37419e-11
MA0081.10.0919
MA0083.10.0895
MA0084.10.55
MA0087.10.487
MA0088.10.653
MA0090.10.277
MA0091.10.0141
MA0092.10.0476
MA0093.10.357
MA0099.24.0077e-11
MA0100.10.369
MA0101.10.13
MA0102.20.00262
MA0103.10.182
MA0104.20.693
MA0105.19.89611e-4
MA0106.10.451
MA0107.10.0662
MA0108.20.00496
MA0111.10.705
MA0112.21.36285e-5
MA0113.10.0982
MA0114.10.589
MA0115.10.403
MA0116.10.00753
MA0117.10.846
MA0119.10.00165
MA0122.10.805
MA0124.10.803
MA0125.10.0101
MA0131.10.907
MA0135.10.133
MA0136.17.92993e-9
MA0137.20.41
MA0138.20.569
MA0139.10.915
MA0140.10.432
MA0141.10.477
MA0142.12.92588e-14
MA0143.14.44629e-6
MA0144.10.0533
MA0145.10.138
MA0146.10.216
MA0147.10.768
MA0148.10.0531
MA0149.10.125
MA0150.10.00136
MA0152.10.496
MA0153.10.926
MA0154.10.032
MA0155.10.845
MA0156.10.00275
MA0157.10.17
MA0159.10.0671
MA0160.10.293
MA0162.10.594
MA0163.11.389e-6
MA0164.10.758
MA0258.10.0162
MA0259.10.755



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: CNhs12837

Novel motifP-value
10.0914
100.0237
1000.909
1010.232
1020.709
1030.216
1040.583
1050.202
1060.0158
1070.25
1080.653
1090.377
110.11
1100.256
1110.0181
1120.221
1130.0426
1140.0189
1150.522
1160.959
1170.235
1180.618
1190.141
120.973
1200.976
1210.991
1220.65
1230.0948
1240.132
1250.815
1260.673
1270.719
1280.43
1290.378
130.605
1300.0648
1310.583
1320.667
1330.0261
1340.557
1350.0256
1360.2
1370.355
1380.248
1390.00955
140.636
1400.149
1410.819
1420.534
1430.0086
1440.494
1450.386
1460.413
1470.676
1486.60288e-4
1490.0099
150.0768
1500.616
1510.0808
1520.367
1530.235
1540.198
1550.815
1560.795
1570.962
1580.447
1590.499
160.274
1600.246
1610.886
1620.62
1630.472
1640.212
1650.267
1660.705
1670.0466
1680.232
1695.12032e-4
170.223
180.255
190.103
20.543
200.935
210.41
220.186
230.00971
240.822
250.399
260.212
270.445
280.842
290.771
30.0789
300.886
310.864
320.0254
330.804
340.81
350.313
360.0585
370.238
380.279
390.506
40.99
400.704
410.192
420.241
430.111
440.901
450.699
460.0554
470.575
480.395
490.0841
50.0875
500.874
510.761
520.43
530.184
540.364
550.0497
560.619
570.386
580.0789
590.229
60.676
600.0776
610.903
620.0278
630.105
640.256
650.0752
660.424
670.182
680.824
690.883
70.393
700.00848
710.0353
720.532
730.115
740.265
750.221
760.405
770.251
780.454
790.0857
80.12
800.156
810.224
820.0301
830.88
840.816
850.0216
860.534
870.262
880.549
890.132
90.219
900.24
910.15
920.0314
930.528
940.0531
950.848
960.0361
970.719
980.305
990.622



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: CNhs12837


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)
0000034 (stem cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002321 (embryonic cell)
0002322 (embryonic stem cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0001062 (anatomical entity)

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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