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FF:10176-103C5: 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 17:15, 29 March 2012


Name:putamen, 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
tissueputamen
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-Neural0.339
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-penis0.854
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-lymphoma-0.309
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12324

Jaspar motifP-value
MA0002.20.0083
MA0003.10.255
MA0004.10.438
MA0006.10.248
MA0007.10.33
MA0009.10.257
MA0014.10.753
MA0017.10.00185
MA0018.20.19
MA0019.10.603
MA0024.10.947
MA0025.10.579
MA0027.10.372
MA0028.10.0984
MA0029.10.0254
MA0030.10.92
MA0031.10.479
MA0035.20.0104
MA0038.10.232
MA0039.20.144
MA0040.10.788
MA0041.10.613
MA0042.10.993
MA0043.10.66
MA0046.10.00728
MA0047.20.0207
MA0048.10.176
MA0050.10.00718
MA0051.10.0412
MA0052.10.525
MA0055.10.00252
MA0057.10.872
MA0058.10.366
MA0059.10.104
MA0060.10.492
MA0061.10.00702
MA0062.20.00559
MA0065.29.57843e-4
MA0066.10.0215
MA0067.10.634
MA0068.10.877
MA0069.10.804
MA0070.10.443
MA0071.10.0166
MA0072.10.149
MA0073.10.286
MA0074.10.303
MA0076.10.247
MA0077.10.471
MA0078.10.697
MA0079.20.534
MA0080.23.01016e-10
MA0081.10.0204
MA0083.10.0101
MA0084.10.815
MA0087.10.809
MA0088.10.204
MA0090.10.171
MA0091.10.137
MA0092.10.249
MA0093.10.444
MA0099.23.59434e-17
MA0100.10.758
MA0101.10.00496
MA0102.20.219
MA0103.10.355
MA0104.20.53
MA0105.10.00258
MA0106.10.0156
MA0107.10.00488
MA0108.20.0881
MA0111.10.55
MA0112.28.84245e-4
MA0113.10.423
MA0114.10.00284
MA0115.10.859
MA0116.10.0117
MA0117.10.826
MA0119.10.0638
MA0122.10.611
MA0124.10.861
MA0125.10.344
MA0131.10.994
MA0135.10.0545
MA0136.18.07754e-14
MA0137.20.804
MA0138.20.551
MA0139.10.373
MA0140.10.00194
MA0141.10.00846
MA0142.10.89
MA0143.10.831
MA0144.10.421
MA0145.10.107
MA0146.10.0158
MA0147.10.411
MA0148.10.0202
MA0149.10.0133
MA0150.12.50392e-4
MA0152.10.809
MA0153.10.414
MA0154.10.041
MA0155.10.644
MA0156.16.88006e-8
MA0157.10.141
MA0159.10.019
MA0160.10.0171
MA0162.10.122
MA0163.17.0597e-5
MA0164.10.753
MA0258.10.0138
MA0259.10.981



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: CNhs12324

Novel motifP-value
10.0668
100.0449
1000.34
1010.378
1020.66
1030.132
1040.134
1050.125
1060.0244
1070.0954
1080.94
1090.00515
110.0152
1100.0561
1110.199
1120.452
1130.631
1140.204
1150.735
1160.18
1170.0113
1180.188
1190.146
120.831
1200.171
1210.236
1220.96
1230.712
1240.165
1250.47
1260.0289
1270.298
1280.163
1290.411
130.00154
1300.279
1310.125
1320.723
1330.00964
1340.715
1350.346
1360.0114
1370.556
1380.919
1390.198
140.783
1400.612
1410.469
1420.768
1430.0195
1440.84
1450.152
1460.308
1470.988
1480.111
1490.245
150.0746
1500.144
1510.521
1520.0674
1530.734
1540.352
1550.765
1560.47
1570.414
1580.664
1590.0589
160.0684
1600.215
1610.295
1620.83
1630.933
1640.0345
1650.0426
1660.942
1670.86
1680.221
1690.00969
170.117
180.168
190.113
20.768
200.179
210.144
220.147
230.22
240.0478
250.461
262.46237e-4
270.643
280.767
290.0186
30.0544
300.99
310.769
320.0343
330.0609
340.621
350.816
360.128
370.0385
380.293
390.231
40.751
400.026
410.346
420.285
430.0973
440.255
450.597
460.0773
470.0685
480.0556
490.168
50.372
500.28
510.469
520.433
530.956
540.382
550.41
560.494
570.31
580.297
590.0684
60.944
600.0472
610.12
620.162
630.17
640.184
650.185
660.147
670.31
680.122
690.359
70.0504
700.046
710.0101
720.361
730.0275
740.653
750.0388
760.517
770.132
780.00207
790.231
80.062
800.503
810.639
820.587
830.0667
840.892
850.196
860.225
878.58404e-4
880.797
890.481
90.347
900.0723
910.407
920.471
930.954
940.239
950.0239
960.783
970.66
980.258
990.537



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: CNhs12324


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)
0000062 (organ)
0000064 (organ part)
0000073 (regional part of nervous system)
0000125 (neural nucleus)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
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)
0001869 (cerebral hemisphere)
0001874 (putamen)
0001890 (forebrain)
0001893 (telencephalon)
0002020 (gray matter)
0002050 (embryonic structure)
0002308 (nucleus of brain)
0002346 (neurectoderm)
0002420 (basal ganglion)
0002435 (striatum)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0003528 (brain grey matter)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005382 (dorsal striatum)
0005383 (caudate-putamen)
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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