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FF:10171-103B9: 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:parietal lobe - 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
tissueparietal lobe
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-Neural0.409
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-penis0.574
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-0.33
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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: CNhs13797

Jaspar motifP-value
MA0002.20.0799
MA0003.10.303
MA0004.10.352
MA0006.10.229
MA0007.10.321
MA0009.10.357
MA0014.10.592
MA0017.10.00253
MA0018.20.1
MA0019.10.807
MA0024.10.699
MA0025.10.991
MA0027.10.539
MA0028.10.0385
MA0029.10.0272
MA0030.10.954
MA0031.10.629
MA0035.20.0276
MA0038.10.575
MA0039.20.0515
MA0040.10.864
MA0041.10.54
MA0042.10.917
MA0043.10.934
MA0046.10.00359
MA0047.20.0332
MA0048.10.078
MA0050.17.18624e-4
MA0051.10.0177
MA0052.10.64
MA0055.10.00124
MA0057.10.891
MA0058.10.287
MA0059.10.134
MA0060.10.832
MA0061.10.0042
MA0062.23.51481e-4
MA0065.24.15726e-4
MA0066.10.0336
MA0067.10.772
MA0068.10.281
MA0069.10.588
MA0070.10.439
MA0071.10.0215
MA0072.10.12
MA0073.10.45
MA0074.10.191
MA0076.10.0616
MA0077.10.0547
MA0078.10.824
MA0079.20.819
MA0080.21.7011e-10
MA0081.10.0148
MA0083.10.0203
MA0084.10.686
MA0087.10.575
MA0088.10.182
MA0090.10.276
MA0091.10.441
MA0092.10.357
MA0093.10.352
MA0099.22.04888e-21
MA0100.10.445
MA0101.13.91649e-4
MA0102.20.0371
MA0103.10.243
MA0104.20.557
MA0105.10.00686
MA0106.10.0441
MA0107.10.00129
MA0108.20.149
MA0111.10.61
MA0112.20.00171
MA0113.10.459
MA0114.10.00208
MA0115.11
MA0116.10.0162
MA0117.10.995
MA0119.10.076
MA0122.10.589
MA0124.10.899
MA0125.10.353
MA0131.10.83
MA0135.10.0923
MA0136.12.92859e-15
MA0137.20.733
MA0138.20.134
MA0139.10.519
MA0140.10.00514
MA0141.10.0119
MA0142.10.697
MA0143.10.537
MA0144.10.414
MA0145.10.177
MA0146.10.00509
MA0147.10.453
MA0148.10.0453
MA0149.10.0426
MA0150.12.12426e-4
MA0152.10.549
MA0153.10.106
MA0154.10.0737
MA0155.10.523
MA0156.11.72023e-11
MA0157.10.537
MA0159.10.00746
MA0160.10.0333
MA0162.10.158
MA0163.11.62681e-4
MA0164.10.9
MA0258.10.0153
MA0259.10.984



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: CNhs13797

Novel motifP-value
10.109
100.0517
1000.352
1010.361
1020.752
1030.212
1040.22
1050.2
1060.0254
1070.0807
1080.803
1090.00209
110.0159
1100.063
1110.47
1120.71
1130.319
1140.562
1150.89
1160.118
1170.0109
1180.167
1190.264
120.372
1200.234
1210.228
1220.932
1230.746
1240.0124
1250.349
1260.0205
1270.546
1280.178
1290.65
133.39183e-4
1300.0877
1310.0293
1320.682
1330.0182
1340.75
1350.0413
1366.68062e-4
1370.783
1380.936
1390.181
140.783
1400.874
1410.86
1420.979
1430.119
1440.868
1450.129
1460.391
1470.818
1480.432
1490.26
150.091
1500.0979
1510.655
1520.0462
1530.89
1540.308
1550.962
1560.455
1570.332
1580.132
1590.0124
160.0592
1600.37
1610.196
1620.467
1630.712
1640.022
1650.0511
1660.771
1670.608
1680.431
1690.0125
170.106
180.282
190.204
20.736
200.0945
210.0848
220.158
230.422
240.0108
250.442
261.69127e-5
270.974
280.696
290.0111
30.0432
300.986
310.997
320.0123
330.0493
340.487
350.799
360.269
370.0296
380.339
390.137
40.898
400.0516
410.452
420.251
430.123
440.281
450.587
460.0791
470.108
480.048
490.243
50.878
500.163
510.544
520.535
530.961
540.4
550.604
560.473
570.474
580.425
590.0673
60.941
600.0667
610.0392
620.252
630.165
640.278
650.236
660.15
670.42
680.146
690.649
70.0494
700.0934
710.00944
720.379
730.0154
740.726
750.0395
760.462
770.123
780.00184
790.492
80.105
800.443
810.824
820.753
830.0164
840.519
850.392
860.177
874.76243e-5
880.699
890.625
90.274
900.356
910.996
920.898
930.654
940.238
950.00882
960.935
970.625
980.29
990.644



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: CNhs13797


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)
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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