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FF:10160-103A7: 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 17:14, 29 March 2012


Name:pineal gland, adult, donor10252
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepineal gland
dev stageNA
sexfemale
age76
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
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-penis0.481
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
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: CNhs12228

Jaspar motifP-value
MA0002.20.0339
MA0003.10.28
MA0004.10.341
MA0006.10.255
MA0007.10.207
MA0009.10.243
MA0014.10.707
MA0017.10.00368
MA0018.20.00267
MA0019.10.718
MA0024.10.96
MA0025.10.495
MA0027.10.891
MA0028.10.885
MA0029.10.517
MA0030.10.223
MA0031.10.574
MA0035.20.155
MA0038.10.052
MA0039.20.26
MA0040.10.45
MA0041.10.583
MA0042.10.827
MA0043.10.38
MA0046.10.0975
MA0047.20.0451
MA0048.10.158
MA0050.10.0702
MA0051.10.0397
MA0052.10.169
MA0055.10.0552
MA0057.10.538
MA0058.10.275
MA0059.10.0243
MA0060.10.0288
MA0061.10.00884
MA0062.20.244
MA0065.20.00275
MA0066.10.0944
MA0067.10.42
MA0068.10.157
MA0069.10.773
MA0070.10.968
MA0071.10.49
MA0072.10.106
MA0073.10.502
MA0074.10.336
MA0076.10.587
MA0077.10.756
MA0078.10.724
MA0079.20.941
MA0080.22.82078e-8
MA0081.10.0939
MA0083.10.0085
MA0084.10.849
MA0087.10.704
MA0088.10.512
MA0090.10.161
MA0091.10.395
MA0092.10.195
MA0093.10.372
MA0099.26.1537e-14
MA0100.10.626
MA0101.10.00555
MA0102.20.185
MA0103.10.162
MA0104.20.429
MA0105.10.00232
MA0106.10.0765
MA0107.10.00531
MA0108.20.214
MA0111.10.79
MA0112.20.00256
MA0113.10.251
MA0114.10.0164
MA0115.10.924
MA0116.10.0139
MA0117.10.951
MA0119.10.175
MA0122.10.693
MA0124.10.214
MA0125.10.341
MA0131.10.674
MA0135.10.0153
MA0136.13.35787e-8
MA0137.20.743
MA0138.20.708
MA0139.10.619
MA0140.10.145
MA0141.10.019
MA0142.10.898
MA0143.10.814
MA0144.10.0527
MA0145.10.21
MA0146.10.0292
MA0147.10.224
MA0148.10.033
MA0149.10.0929
MA0150.10.00149
MA0152.10.894
MA0153.10.347
MA0154.10.0278
MA0155.10.331
MA0156.11.47004e-5
MA0157.10.484
MA0159.10.0325
MA0160.10.0844
MA0162.10.0494
MA0163.16.35692e-5
MA0164.10.308
MA0258.10.0419
MA0259.10.702



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: CNhs12228

Novel motifP-value
10.143
100.0538
1000.212
1010.766
1020.95
1030.0347
1040.191
1050.816
1060.00426
1070.00833
1080.631
1090.00785
110.028
1100.0982
1110.0415
1120.791
1130.437
1140.308
1150.654
1160.292
1170.031
1180.0458
1190.236
120.935
1200.153
1210.566
1220.827
1230.811
1240.294
1250.576
1260.365
1270.883
1280.0795
1290.352
130.0193
1300.551
1310.0668
1320.506
1330.0625
1340.539
1350.88
1360.00727
1370.833
1380.332
1390.55
140.752
1400.116
1410.504
1420.68
1430.133
1440.571
1450.0881
1460.309
1470.365
1480.033
1490.187
150.0338
1500.192
1510.462
1520.0186
1530.884
1540.732
1550.749
1560.498
1570.368
1580.0159
1590.0066
160.0526
1600.0375
1610.0753
1620.497
1630.593
1640.0176
1650.0505
1660.819
1670.412
1680.588
1690.019
170.0348
180.0952
190.224
20.716
200.264
210.186
220.254
230.202
240.158
250.398
264.92845e-4
270.604
280.812
290.0114
30.0927
300.807
310.867
320.0067
330.076
340.64
350.807
360.164
370.083
380.332
390.173
40.996
400.0253
410.153
420.461
430.117
440.136
450.714
460.0492
470.183
480.136
490.227
50.37
500.3
510.302
520.277
530.855
540.36
550.789
560.487
570.179
580.376
590.0546
60.686
600.0538
610.0605
620.377
630.0564
640.414
650.12
660.218
670.36
680.12
690.0411
70.168
700.00411
710.0118
720.655
730.0244
740.767
750.0639
760.282
770.159
780.0745
790.365
80.00915
800.843
810.256
820.648
830.17
840.415
850.0853
860.5
878.57144e-5
880.917
890.151
90.632
900.241
910.575
920.301
930.911
940.0702
950.015
960.767
970.698
980.205
990.477



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: CNhs12228


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)
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)
0000949 (endocrine system)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001890 (forebrain)
0001894 (diencephalon)
0001899 (epithalamus)
0001905 (pineal body)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002757 (regional part of epithalamus)
0002780 (regional part of forebrain)
0002784 (regional part of diencephalon)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0003296 (gland of diencephalon)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005408 (circumventricular organ)
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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