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FF:11352-117H2: 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 16:48, 29 March 2012


Name:Neural stem cells, donor2
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 stage18 weeks old fetus
sexunknown
ageembryo 18week
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 number2649
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-Neural0.362
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-penis0.0367
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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: CNhs11384

Jaspar motifP-value
MA0002.29.23419e-4
MA0003.10.188
MA0004.10.442
MA0006.10.476
MA0007.10.0806
MA0009.10.107
MA0014.10.465
MA0017.10.00388
MA0018.20.005
MA0019.10.991
MA0024.10.00918
MA0025.10.626
MA0027.10.28
MA0028.10.675
MA0029.10.563
MA0030.10.394
MA0031.10.584
MA0035.20.423
MA0038.11.98879e-5
MA0039.20.198
MA0040.10.949
MA0041.10.316
MA0042.10.564
MA0043.10.0889
MA0046.10.632
MA0047.20.0955
MA0048.10.415
MA0050.11.84303e-6
MA0051.10.00706
MA0052.10.586
MA0055.10.0682
MA0057.10.425
MA0058.10.385
MA0059.10.14
MA0060.12.9585e-7
MA0061.10.0738
MA0062.20.178
MA0065.20.00116
MA0066.10.109
MA0067.10.784
MA0068.10.0128
MA0069.10.926
MA0070.10.0198
MA0071.10.0289
MA0072.10.769
MA0073.10.467
MA0074.10.184
MA0076.10.957
MA0077.10.115
MA0078.10.238
MA0079.20.799
MA0080.22.35073e-8
MA0081.10.151
MA0083.10.56
MA0084.10.415
MA0087.10.446
MA0088.10.225
MA0090.10.0681
MA0091.10.465
MA0092.10.48
MA0093.10.515
MA0099.24.72777e-6
MA0100.10.322
MA0101.10.099
MA0102.20.0472
MA0103.10.0363
MA0104.20.716
MA0105.10.0205
MA0106.10.0999
MA0107.10.121
MA0108.20.239
MA0111.10.536
MA0112.22.48492e-4
MA0113.10.0421
MA0114.10.0215
MA0115.10.0865
MA0116.10.013
MA0117.10.8
MA0119.10.158
MA0122.10.604
MA0124.10.366
MA0125.10.0325
MA0131.10.882
MA0135.10.0714
MA0136.13.18955e-5
MA0137.20.687
MA0138.20.615
MA0139.10.383
MA0140.10.0492
MA0141.10.00214
MA0142.10.0538
MA0143.10.0226
MA0144.10.315
MA0145.10.188
MA0146.10.0117
MA0147.10.572
MA0148.10.105
MA0149.10.0176
MA0150.10.00215
MA0152.10.964
MA0153.10.797
MA0154.10.0352
MA0155.10.473
MA0156.11.11616e-4
MA0157.10.0674
MA0159.10.00285
MA0160.10.0245
MA0162.10.129
MA0163.14.01391e-5
MA0164.10.476
MA0258.10.0108
MA0259.10.886



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: CNhs11384

Novel motifP-value
10.0579
100.0838
1000.406
1010.571
1020.808
1030.341
1040.153
1050.792
1060.0363
1070.114
1080.615
1099.12025e-4
110.015
1100.167
1110.114
1120.0826
1130.758
1140.00589
1150.723
1160.262
1170.0213
1180.154
1190.12
120.938
1200.643
1210.493
1220.935
1230.556
1240.0331
1250.93
1260.0328
1270.324
1280.248
1290.8
130.015
1300.66
1310.749
1320.862
1330.417
1340.765
1350.567
1360.00654
1370.394
1380.558
1390.177
140.679
1400.131
1410.45
1420.657
1430.0188
1440.731
1450.366
1460.88
1470.938
1480.0686
1490.0333
150.119
1500.219
1510.434
1520.0333
1530.725
1540.699
1550.31
1560.247
1570.271
1580.773
1590.723
160.0273
1600.108
1610.243
1620.794
1630.728
1640.0108
1650.639
1660.925
1670.188
1680.438
1690.0122
170.0757
180.387
190.159
20.697
200.301
210.0211
220.132
230.23
240.142
250.633
260.00837
270.506
280.922
290.0244
30.0288
300.843
310.831
320.0119
330.305
340.747
350.65
360.182
370.0268
380.214
390.2
40.529
400.0457
410.938
420.196
430.163
440.0129
450.752
460.127
470.0539
480.0516
490.245
50.274
500.332
510.598
520.639
530.888
540.464
550.264
560.335
570.477
580.196
590.04
60.445
600.0862
610.0194
620.156
630.0989
640.29
650.143
660.992
670.692
680.545
690.247
70.269
700.00985
710.0095
720.3
730.00944
740.131
750.0327
760.266
770.0851
780.0119
790.00711
80.0481
800.802
810.375
820.136
830.157
840.668
850.0615
860.332
870.0236
880.543
890.571
90.46
900.763
910.877
920.28
930.738
940.118
950.00183
960.978
970.912
980.359
990.348



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: CNhs11384


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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