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FF:11275-116H6: 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 16:38, 29 March 2012


Name:Neural stem 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
tissuebrain
dev stage19 weeks old fetus
sexunknown
ageembryo 19week
cell typeneural stem cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2457
catalog numbercustom
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-Neural0.0983
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-penis0.0815
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-lymphoma0.364
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C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
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: CNhs11063

Jaspar motifP-value
MA0002.28.49285e-4
MA0003.10.162
MA0004.10.21
MA0006.10.918
MA0007.10.171
MA0009.10.0487
MA0014.10.309
MA0017.10.00418
MA0018.20.724
MA0019.10.65
MA0024.10.00234
MA0025.10.764
MA0027.10.432
MA0028.10.68
MA0029.10.0641
MA0030.10.615
MA0031.10.0913
MA0035.20.0218
MA0038.13.63756e-4
MA0039.20.0349
MA0040.10.554
MA0041.10.352
MA0042.10.646
MA0043.10.561
MA0046.10.427
MA0047.20.00467
MA0048.10.457
MA0050.11.02795e-4
MA0051.10.051
MA0052.10.523
MA0055.10.00265
MA0057.10.407
MA0058.10.143
MA0059.10.0435
MA0060.17.23315e-4
MA0061.10.0184
MA0062.20.0985
MA0065.20.00159
MA0066.10.0925
MA0067.10.57
MA0068.10.0155
MA0069.10.893
MA0070.10.122
MA0071.10.035
MA0072.10.411
MA0073.10.741
MA0074.10.297
MA0076.10.997
MA0077.10.24
MA0078.10.39
MA0079.20.996
MA0080.24.36396e-10
MA0081.10.124
MA0083.10.224
MA0084.10.876
MA0087.10.596
MA0088.10.129
MA0090.10.133
MA0091.10.178
MA0092.10.631
MA0093.10.254
MA0099.23.97624e-5
MA0100.10.382
MA0101.10.0195
MA0102.20.044
MA0103.10.00589
MA0104.20.264
MA0105.10.00481
MA0106.10.234
MA0107.10.0164
MA0108.20.278
MA0111.10.628
MA0112.22.44986e-4
MA0113.10.0634
MA0114.10.02
MA0115.10.673
MA0116.10.00575
MA0117.10.844
MA0119.10.0819
MA0122.10.961
MA0124.10.651
MA0125.10.00303
MA0131.10.833
MA0135.10.0103
MA0136.12.19763e-7
MA0137.20.805
MA0138.20.464
MA0139.10.411
MA0140.10.0066
MA0141.10.00415
MA0142.13.78465e-4
MA0143.10.00352
MA0144.10.247
MA0145.10.397
MA0146.10.0197
MA0147.10.179
MA0148.10.0344
MA0149.10.00601
MA0150.15.45638e-4
MA0152.10.47
MA0153.10.769
MA0154.10.0272
MA0155.10.631
MA0156.19.76896e-5
MA0157.10.0345
MA0159.10.00848
MA0160.10.0126
MA0162.10.144
MA0163.13.72898e-4
MA0164.10.631
MA0258.10.0101
MA0259.10.525



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: CNhs11063

Novel motifP-value
10.0429
100.0934
1000.36
1010.734
1020.73
1030.227
1040.133
1050.565
1060.129
1070.693
1080.591
1090.00328
110.0151
1100.0823
1110.0477
1120.0984
1130.82
1140.00799
1150.749
1160.356
1170.0185
1180.0934
1190.0875
120.892
1200.961
1210.557
1220.653
1230.247
1240.196
1250.895
1260.113
1270.068
1280.708
1290.417
130.0182
1300.467
1310.727
1320.742
1330.251
1340.693
1350.791
1360.106
1370.535
1380.396
1390.0176
140.794
1400.143
1410.661
1420.501
1430.0266
1440.777
1450.865
1460.665
1470.865
1480.269
1490.309
150.063
1500.321
1510.503
1520.075
1530.951
1540.64
1550.0918
1560.159
1570.706
1580.639
1590.326
160.0786
1600.086
1610.0764
1620.709
1630.88
1640.00592
1650.615
1660.922
1670.397
1680.599
1690.0133
170.073
180.36
190.29
20.812
200.264
210.125
220.245
230.298
240.611
250.539
260.018
270.64
280.878
290.0367
30.04
300.813
310.935
320.0237
330.286
340.693
350.764
360.0843
370.0342
380.117
390.549
40.968
400.0282
410.601
420.181
430.162
440.0819
450.867
460.102
470.042
480.067
490.122
50.257
500.581
510.497
520.732
530.721
540.379
550.409
560.411
570.289
580.148
590.111
60.558
600.135
610.0339
620.11
630.166
640.185
650.0949
660.972
670.561
680.5
690.554
70.27
700.0204
710.0358
720.494
730.0223
740.231
750.0235
760.236
770.064
780.0449
790.347
80.102
800.915
810.479
820.263
830.743
840.642
850.0926
860.402
870.0644
880.933
890.562
90.568
900.599
910.978
920.139
930.299
940.0825
950.0115
960.922
970.801
980.0948
990.911



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: CNhs11063


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)
0000047 (neuronal stem cell)
0000048 (multi fate stem cell)
0000133 (neurectodermal cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)

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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