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FF:10193-103E4: 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 17:23, 29 March 2012


Name:diencephalon, adult
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuediencephalon
dev stageNA
sexmale
age26
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberR1234049-10
sample typeNA
extraction protocol (Details)NA
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-Neural0.167
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-penis0.256
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-0.356
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0.337
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs12610

Jaspar motifP-value
MA0002.20.00533
MA0003.10.367
MA0004.10.395
MA0006.10.46
MA0007.10.354
MA0009.10.105
MA0014.10.693
MA0017.10.0118
MA0018.20.142
MA0019.10.46
MA0024.10.882
MA0025.10.319
MA0027.10.477
MA0028.10.0721
MA0029.10.0381
MA0030.10.212
MA0031.10.966
MA0035.20.0231
MA0038.10.0605
MA0039.20.135
MA0040.10.438
MA0041.10.326
MA0042.10.695
MA0043.10.799
MA0046.10.0543
MA0047.20.2
MA0048.10.0591
MA0050.10.00382
MA0051.10.128
MA0052.10.661
MA0055.12.23573e-4
MA0057.10.948
MA0058.10.436
MA0059.10.107
MA0060.10.333
MA0061.10.00366
MA0062.20.00451
MA0065.20.00384
MA0066.10.051
MA0067.10.847
MA0068.10.0569
MA0069.10.57
MA0070.10.0928
MA0071.10.0246
MA0072.10.508
MA0073.10.558
MA0074.10.318
MA0076.10.149
MA0077.10.062
MA0078.10.724
MA0079.20.414
MA0080.29.46668e-9
MA0081.10.0393
MA0083.10.0374
MA0084.10.653
MA0087.10.241
MA0088.10.121
MA0090.10.156
MA0091.10.826
MA0092.10.313
MA0093.10.457
MA0099.21.31105e-17
MA0100.10.567
MA0101.10.00167
MA0102.20.0568
MA0103.10.207
MA0104.20.478
MA0105.13.0824e-4
MA0106.10.0187
MA0107.10.00195
MA0108.20.88
MA0111.10.488
MA0112.20.00161
MA0113.10.187
MA0114.10.00856
MA0115.10.867
MA0116.10.0036
MA0117.10.818
MA0119.10.0446
MA0122.10.747
MA0124.10.879
MA0125.10.272
MA0131.10.619
MA0135.10.0105
MA0136.11.35668e-12
MA0137.20.777
MA0138.20.0966
MA0139.10.467
MA0140.10.013
MA0141.10.0346
MA0142.10.545
MA0143.10.0739
MA0144.10.543
MA0145.10.31
MA0146.10.00946
MA0147.10.325
MA0148.10.221
MA0149.10.00669
MA0150.13.44588e-5
MA0152.10.82
MA0153.10.819
MA0154.10.0503
MA0155.10.97
MA0156.15.57529e-7
MA0157.10.457
MA0159.10.0224
MA0160.10.069
MA0162.10.172
MA0163.11.2202e-6
MA0164.10.529
MA0258.10.0195
MA0259.10.753



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: CNhs12610

Novel motifP-value
10.0541
100.0246
1000.252
1010.857
1020.814
1030.309
1040.0693
1050.0848
1060.0468
1070.14
1080.789
1090.00992
110.00989
1100.0417
1110.145
1120.566
1130.739
1140.158
1150.67
1160.229
1170.00596
1180.198
1190.162
120.627
1200.173
1210.461
1220.426
1230.198
1240.0716
1250.737
1260.0761
1270.453
1280.303
1290.875
137.39237e-4
1300.606
1310.0294
1320.806
1330.0033
1340.527
1350.175
1360.0121
1370.75
1380.911
1390.165
140.794
1400.256
1410.431
1420.954
1430.0127
1440.876
1450.133
1460.457
1470.725
1480.595
1490.493
150.0736
1500.135
1510.71
1520.11
1530.509
1540.606
1550.31
1560.366
1570.384
1580.449
1590.343
160.0798
1600.269
1610.268
1620.947
1630.933
1640.00597
1650.104
1660.658
1670.435
1680.67
1690.012
170.137
180.303
190.274
20.95
200.0423
210.0348
220.285
230.46
240.132
250.564
262.09811e-4
270.958
280.786
290.0103
30.018
300.557
310.896
320.0274
330.0617
340.74
350.614
360.107
370.0351
380.361
390.36
40.882
400.0441
410.546
420.13
430.108
440.486
450.816
460.0457
470.0889
480.0563
490.122
50.648
500.247
510.561
520.758
530.842
540.482
550.599
560.512
570.208
580.321
590.188
60.885
600.0862
610.0705
620.212
630.183
640.181
650.294
660.15
670.313
680.318
690.4
70.0804
700.0283
710.00658
720.427
730.0345
740.793
750.0169
760.218
770.242
780.00107
790.19
80.0806
800.715
810.633
820.587
830.281
840.542
850.338
860.216
870.0187
880.843
890.676
90.533
900.0737
910.299
920.375
930.787
940.0676
950.0302
960.824
970.642
980.123
990.81



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: CNhs12610


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)
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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