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FF:10072-101I9: 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 16:53, 29 March 2012


Name:parietal lobe, fetal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueparietal lobe
dev stage20 weeks fetus
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA601609
catalog numberCat:RtHFN: Brain parietal lobe
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-Neural0.989
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-penis0.0428
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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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: CNhs11782

Jaspar motifP-value
MA0002.20.00237
MA0003.10.162
MA0004.10.419
MA0006.10.215
MA0007.10.139
MA0009.10.447
MA0014.10.577
MA0017.10.00137
MA0018.20.249
MA0019.10.147
MA0024.10.0576
MA0025.10.0465
MA0027.10.498
MA0028.10.357
MA0029.10.116
MA0030.10.373
MA0031.10.0338
MA0035.20.0119
MA0038.10.208
MA0039.20.0897
MA0040.10.539
MA0041.10.367
MA0042.10.53
MA0043.10.639
MA0046.10.0219
MA0047.20.002
MA0048.10.678
MA0050.11.22575e-4
MA0051.10.00661
MA0052.10.17
MA0055.10.0817
MA0057.10.251
MA0058.10.268
MA0059.10.204
MA0060.10.178
MA0061.10.0177
MA0062.20.0443
MA0065.22.54589e-4
MA0066.10.0156
MA0067.10.789
MA0068.10.485
MA0069.10.432
MA0070.10.485
MA0071.10.0362
MA0072.10.249
MA0073.10.27
MA0074.10.158
MA0076.10.614
MA0077.10.262
MA0078.10.732
MA0079.20.694
MA0080.22.56919e-11
MA0081.10.0512
MA0083.10.00672
MA0084.10.672
MA0087.10.237
MA0088.10.235
MA0090.10.194
MA0091.10.231
MA0092.10.299
MA0093.10.416
MA0099.25.73612e-23
MA0100.10.938
MA0101.10.00833
MA0102.20.00925
MA0103.10.171
MA0104.20.743
MA0105.10.0173
MA0106.10.0667
MA0107.10.0081
MA0108.20.224
MA0111.10.819
MA0112.21.53311e-4
MA0113.10.0363
MA0114.10.00491
MA0115.10.463
MA0116.10.0231
MA0117.10.806
MA0119.10.174
MA0122.10.27
MA0124.10.709
MA0125.10.296
MA0131.10.617
MA0135.10.652
MA0136.11.04131e-13
MA0137.20.124
MA0138.20.706
MA0139.10.268
MA0140.10.00119
MA0141.10.0022
MA0142.10.569
MA0143.10.466
MA0144.10.0617
MA0145.10.0861
MA0146.10.0145
MA0147.10.633
MA0148.10.0162
MA0149.10.0144
MA0150.11.42916e-5
MA0152.10.298
MA0153.10.317
MA0154.10.0264
MA0155.10.437
MA0156.17.73699e-8
MA0157.10.0338
MA0159.10.00214
MA0160.10.00402
MA0162.10.217
MA0163.15.67103e-4
MA0164.10.892
MA0258.10.00559
MA0259.10.832



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: CNhs11782

Novel motifP-value
10.0913
100.138
1000.608
1010.62
1020.857
1030.0509
1040.0913
1050.144
1060.0295
1070.0954
1080.868
1094.41781e-4
110.0397
1100.17
1110.388
1120.249
1130.329
1140.075
1150.947
1160.239
1170.0322
1180.268
1190.35
120.506
1200.282
1210.333
1220.496
1230.0991
1240.317
1250.46
1260.0193
1270.179
1280.18
1290.348
130.00632
1300.0511
1310.646
1320.771
1330.298
1340.808
1350.699
1360.00528
1370.266
1380.866
1390.0711
140.68
1400.405
1410.57
1420.802
1430.0124
1440.846
1450.368
1460.392
1470.7
1480.026
1490.124
150.113
1500.249
1510.39
1520.0346
1530.813
1540.538
1550.783
1560.43
1570.444
1580.381
1590.105
160.0323
1600.241
1610.208
1620.445
1630.583
1640.116
1650.219
1660.813
1670.995
1680.0885
1690.0105
170.096
180.167
190.121
20.471
200.534
210.231
220.0793
230.204
240.0139
250.411
260.0263
270.412
280.747
290.0645
30.0804
300.58
310.578
320.0428
330.144
340.472
350.619
360.219
370.0164
380.239
390.249
40.93
400.0395
410.235
420.236
430.121
440.211
450.478
460.245
470.101
480.108
490.219
50.317
500.318
510.325
520.32
530.963
540.255
550.934
560.4
570.675
580.274
590.0245
60.929
600.0583
610.0559
620.189
630.144
640.472
650.172
660.292
670.73
680.0994
690.747
70.0709
700.0367
710.0273
720.157
730.0124
740.902
750.0565
760.593
770.082
780.0179
790.443
80.12
800.115
810.601
820.359
830.00917
840.902
850.0869
860.255
872.05066e-4
880.769
890.15
90.252
900.394
910.924
920.299
930.481
940.148
950.00719
960.345
970.76
980.268
990.562



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: CNhs11782


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)
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)
0000956 (cerebral cortex)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001872 (parietal lobe)
0001890 (forebrain)
0001893 (telencephalon)
0001950 (neocortex)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002619 (regional part of cerebral cortex)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
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)
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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