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FF:10168-103B6: 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:thalamus - adult, donor10196
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuethalamus
dev stageNA
sexfemale
age60
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
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-Neural0.262
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-penis0.735
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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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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: CNhs13794

Jaspar motifP-value
MA0002.20.0594
MA0003.10.248
MA0004.10.213
MA0006.10.346
MA0007.10.557
MA0009.10.307
MA0014.10.776
MA0017.10.00602
MA0018.20.078
MA0019.10.806
MA0024.10.991
MA0025.10.945
MA0027.10.307
MA0028.10.0228
MA0029.10.0519
MA0030.10.707
MA0031.10.699
MA0035.20.0139
MA0038.10.304
MA0039.20.13
MA0040.10.408
MA0041.10.486
MA0042.10.931
MA0043.10.667
MA0046.10.00149
MA0047.20.138
MA0048.10.0722
MA0050.10.0168
MA0051.10.111
MA0052.10.418
MA0055.15.81289e-4
MA0057.10.949
MA0058.10.19
MA0059.10.0633
MA0060.10.746
MA0061.10.00345
MA0062.21.20415e-4
MA0065.20.00222
MA0066.10.0323
MA0067.10.669
MA0068.10.933
MA0069.10.709
MA0070.10.702
MA0071.10.0184
MA0072.10.518
MA0073.10.552
MA0074.10.245
MA0076.10.0298
MA0077.10.0152
MA0078.10.512
MA0079.20.714
MA0080.29.55176e-9
MA0081.10.0389
MA0083.10.029
MA0084.10.141
MA0087.10.173
MA0088.10.235
MA0090.10.275
MA0091.10.427
MA0092.10.285
MA0093.10.234
MA0099.21.20694e-21
MA0100.10.646
MA0101.19.11515e-4
MA0102.20.163
MA0103.10.0839
MA0104.20.414
MA0105.10.0016
MA0106.10.041
MA0107.10.0018
MA0108.20.803
MA0111.10.977
MA0112.20.00129
MA0113.10.51
MA0114.10.0079
MA0115.10.686
MA0116.10.00431
MA0117.10.722
MA0119.10.264
MA0122.10.668
MA0124.10.823
MA0125.10.355
MA0131.10.823
MA0135.10.0802
MA0136.12.1185e-12
MA0137.20.16
MA0138.20.0696
MA0139.10.47
MA0140.10.0272
MA0141.10.0179
MA0142.10.588
MA0143.10.0191
MA0144.10.837
MA0145.10.405
MA0146.10.00569
MA0147.10.25
MA0148.10.215
MA0149.10.0224
MA0150.11.33569e-4
MA0152.10.732
MA0153.10.246
MA0154.10.0568
MA0155.10.486
MA0156.11.69985e-10
MA0157.10.697
MA0159.10.0269
MA0160.10.055
MA0162.10.144
MA0163.12.06449e-6
MA0164.10.965
MA0258.10.0238
MA0259.10.643



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: CNhs13794

Novel motifP-value
10.0784
100.0595
1000.406
1010.432
1020.977
1030.0408
1040.0857
1050.149
1060.0451
1070.147
1080.92
1096.66711e-4
110.009
1100.0367
1110.248
1120.462
1130.233
1140.234
1150.812
1160.125
1170.00457
1180.14
1190.46
120.456
1200.155
1210.345
1220.745
1230.453
1240.0474
1250.68
1260.0452
1270.509
1280.256
1290.354
130.00219
1300.0418
1310.0106
1320.491
1335.98201e-4
1340.643
1350.139
1366.98977e-4
1370.434
1380.899
1390.342
140.907
1400.82
1410.7
1420.81
1430.0534
1440.71
1450.392
1460.496
1470.643
1480.907
1490.126
150.122
1500.0947
1510.915
1520.0644
1530.666
1540.293
1550.818
1560.204
1570.339
1580.0888
1590.0116
160.0309
1600.276
1610.285
1620.489
1630.916
1640.00449
1650.252
1660.682
1670.776
1680.549
1690.021
170.0634
180.05
190.358
20.788
200.104
210.0214
220.171
230.695
240.00729
250.578
263.42914e-4
270.821
280.821
290.00599
30.0399
300.908
310.997
320.00847
330.0669
340.65
350.548
360.411
370.0299
380.434
390.336
40.995
400.108
410.381
420.2
430.141
440.126
450.721
460.0493
470.0792
480.0325
490.421
50.738
500.269
510.39
520.74
530.665
540.477
550.896
560.459
570.56
580.562
590.0538
60.943
600.137
610.0701
620.361
630.216
640.207
650.33
660.122
670.253
680.414
690.91
70.13
700.0353
710.00768
720.389
730.0238
740.929
750.0163
760.167
770.12
780.003
790.477
80.0679
800.657
810.56
820.62
830.0223
840.551
850.568
860.127
879.24487e-5
880.545
890.219
90.326
900.142
910.817
920.979
930.96
940.201
950.0063
960.994
970.7
980.329
990.638



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: CNhs13794


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

UBERON: Anatomy
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001890 (forebrain)
0001894 (diencephalon)
0001897 (dorsal plus ventral thalamus)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
0007135 (neural keel)
0007284 (presumptive neural plate)

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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