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FF:12725-135G7: 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 Embryoid body cells, melanocytic induction, day00, biol_rep2 (H9EB-2 d0)
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-penis-0.0175
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-lymphoma0.479
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0.0428
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs12825

Jaspar motifP-value
MA0002.25.8575e-7
MA0003.10.0812
MA0004.10.903
MA0006.10.811
MA0007.10.647
MA0009.10.354
MA0014.10.694
MA0017.10.257
MA0018.20.138
MA0019.10.158
MA0024.19.75511e-4
MA0025.10.328
MA0027.10.328
MA0028.10.547
MA0029.10.826
MA0030.10.97
MA0031.10.467
MA0035.20.651
MA0038.13.08219e-4
MA0039.20.0922
MA0040.10.794
MA0041.10.686
MA0042.11
MA0043.10.789
MA0046.10.22
MA0047.20.209
MA0048.10.977
MA0050.13.30188e-7
MA0051.10.00172
MA0052.10.335
MA0055.10.551
MA0057.10.447
MA0058.10.865
MA0059.10.263
MA0060.11.21155e-13
MA0061.10.0122
MA0062.20.646
MA0065.20.18
MA0066.10.18
MA0067.10.477
MA0068.10.0101
MA0069.10.397
MA0070.10.00177
MA0071.10.639
MA0072.10.787
MA0073.10.835
MA0074.10.721
MA0076.10.405
MA0077.10.0939
MA0078.10.688
MA0079.20.0587
MA0080.22.53429e-12
MA0081.10.0458
MA0083.10.58
MA0084.10.424
MA0087.10.574
MA0088.10.185
MA0090.10.534
MA0091.10.0354
MA0092.10.0738
MA0093.10.97
MA0099.24.39916e-8
MA0100.10.804
MA0101.10.0778
MA0102.20.0197
MA0103.10.601
MA0104.20.408
MA0105.12.18242e-5
MA0106.10.578
MA0107.10.0735
MA0108.21.19249e-15
MA0111.10.54
MA0112.28.21824e-6
MA0113.10.0847
MA0114.10.387
MA0115.10.644
MA0116.12.62514e-4
MA0117.10.814
MA0119.15.23278e-4
MA0122.10.861
MA0124.10.987
MA0125.10.00419
MA0131.10.892
MA0135.10.0085
MA0136.19.80357e-10
MA0137.20.606
MA0138.20.553
MA0139.10.606
MA0140.10.471
MA0141.10.159
MA0142.14.59956e-8
MA0143.10.00142
MA0144.10.14
MA0145.10.166
MA0146.10.216
MA0147.10.288
MA0148.10.0433
MA0149.10.00388
MA0150.18.34063e-4
MA0152.10.765
MA0153.10.0845
MA0154.10.00636
MA0155.10.631
MA0156.18.43524e-4
MA0157.10.144
MA0159.10.0654
MA0160.10.141
MA0162.10.43
MA0163.17.7468e-10
MA0164.10.845
MA0258.10.0173
MA0259.10.947



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: CNhs12825

Novel motifP-value
10.0375
100.0104
1000.787
1010.249
1020.811
1030.159
1040.597
1050.266
1060.0486
1070.323
1080.638
1090.08
110.0527
1100.165
1110.00313
1120.215
1130.442
1140.00394
1150.262
1160.645
1170.0902
1180.453
1190.15
120.992
1200.8
1210.993
1220.97
1230.0169
1240.199
1250.259
1260.72
1270.502
1280.363
1290.385
130.39
1300.184
1310.752
1320.978
1330.773
1340.593
1350.141
1360.426
1370.264
1380.13
1390.00618
140.564
1400.0608
1410.301
1420.99
1430.00376
1440.678
1450.293
1460.497
1470.877
1480.0119
1490.024
150.0381
1500.523
1510.116
1520.502
1530.256
1540.231
1550.612
1560.32
1570.693
1580.596
1590.572
160.29
1600.186
1610.467
1620.587
1630.693
1640.103
1650.31
1660.954
1670.00998
1680.295
1695.02787e-4
170.213
180.236
190.221
20.706
200.829
210.353
220.295
230.0965
240.596
250.402
260.0505
270.514
280.695
290.45
30.04
300.542
310.916
320.0697
330.459
340.858
350.23
360.0199
370.133
380.263
390.547
40.953
400.387
410.191
420.153
430.107
440.885
450.794
460.0483
470.2
480.209
490.0718
50.0689
500.961
510.615
520.625
530.173
540.464
550.0245
560.53
570.251
580.0901
590.217
60.581
600.166
610.621
620.0362
630.0738
640.186
650.133
660.477
670.306
680.397
690.824
70.335
700.00537
710.021
720.456
730.118
740.285
750.0876
760.254
770.272
780.354
790.322
80.0737
800.389
810.22
820.0515
830.953
840.834
850.0804
860.26
870.988
880.942
890.123
90.318
900.105
910.187
920.0399
930.205
940.0245
950.657
960.0223
970.548
980.14
990.746



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: CNhs12825


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)
0000055 (non-terminally differentiated cell)
0000066 (epithelial cell)
0000075 (columnar/cuboidal epithelial cell)
0000133 (neurectodermal cell)
0000147 (pigment cell)
0000148 (melanocyte)
0000219 (motile cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000325 (stuff accumulating cell)
0000333 (migratory neural crest cell)
0000541 (melanoblast)
0000548 (animal cell)
0000710 (neurecto-epithelial cell)
0002077 (ecto-epithelial cell)
0002321 (embryonic cell)
0002322 (embryonic stem cell)
0002371 (somatic 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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