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FF:10164-103B2: 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:caudate nucleus, 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
tissuecaudate nucleus
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-Neural0.319
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-penis0.998
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-0.31
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0494
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12321

Jaspar motifP-value
MA0002.20.00579
MA0003.10.277
MA0004.10.455
MA0006.10.281
MA0007.10.335
MA0009.10.2
MA0014.10.76
MA0017.10.00168
MA0018.20.436
MA0019.10.751
MA0024.10.822
MA0025.10.272
MA0027.10.317
MA0028.10.135
MA0029.10.0108
MA0030.10.385
MA0031.10.981
MA0035.20.00658
MA0038.10.32
MA0039.20.239
MA0040.10.818
MA0041.10.725
MA0042.10.826
MA0043.10.743
MA0046.10.0105
MA0047.20.0513
MA0048.10.201
MA0050.10.0479
MA0051.10.132
MA0052.10.396
MA0055.10.00417
MA0057.10.894
MA0058.10.399
MA0059.10.0809
MA0060.10.403
MA0061.10.00752
MA0062.20.0157
MA0065.24.19891e-4
MA0066.10.0141
MA0067.10.737
MA0068.10.548
MA0069.10.597
MA0070.10.462
MA0071.10.0235
MA0072.10.181
MA0073.10.315
MA0074.10.339
MA0076.10.287
MA0077.10.406
MA0078.10.548
MA0079.20.486
MA0080.29.42935e-9
MA0081.10.0351
MA0083.10.0182
MA0084.10.961
MA0087.10.867
MA0088.10.204
MA0090.10.196
MA0091.10.247
MA0092.10.246
MA0093.10.471
MA0099.27.35267e-16
MA0100.10.816
MA0101.10.00956
MA0102.20.334
MA0103.10.259
MA0104.20.48
MA0105.19.2473e-4
MA0106.10.0297
MA0107.10.00822
MA0108.20.127
MA0111.10.511
MA0112.26.48209e-4
MA0113.10.527
MA0114.10.00254
MA0115.10.435
MA0116.10.00762
MA0117.10.79
MA0119.10.0608
MA0122.10.916
MA0124.10.839
MA0125.10.285
MA0131.10.919
MA0135.10.0308
MA0136.14.99455e-12
MA0137.20.453
MA0138.20.702
MA0139.10.368
MA0140.18.76382e-4
MA0141.10.00524
MA0142.10.896
MA0143.10.763
MA0144.10.465
MA0145.10.114
MA0146.10.0219
MA0147.10.343
MA0148.10.0335
MA0149.10.0149
MA0150.12.74942e-4
MA0152.10.638
MA0153.10.427
MA0154.10.0308
MA0155.10.642
MA0156.12.63173e-6
MA0157.10.367
MA0159.10.0115
MA0160.10.0143
MA0162.10.113
MA0163.11.55002e-5
MA0164.10.698
MA0258.10.00861
MA0259.10.937



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: CNhs12321

Novel motifP-value
10.0391
100.0446
1000.332
1010.51
1020.717
1030.119
1040.0874
1050.122
1060.0229
1070.0755
1080.767
1090.00496
110.0137
1100.0599
1110.087
1120.397
1130.74
1140.132
1150.898
1160.18
1170.0131
1180.185
1190.124
120.924
1200.161
1210.269
1220.831
1230.823
1240.332
1250.281
1260.0551
1270.335
1280.103
1290.463
130.00342
1300.417
1310.168
1320.652
1330.0232
1340.77
1350.19
1360.0165
1370.606
1380.925
1390.152
140.795
1400.348
1410.339
1420.55
1430.0196
1440.861
1450.169
1460.456
1470.924
1480.0984
1490.21
150.084
1500.177
1510.499
1520.0741
1530.826
1540.514
1550.686
1560.57
1570.548
1580.763
1590.0493
160.064
1600.197
1610.331
1620.943
1630.901
1640.041
1650.0803
1660.81
1670.619
1680.289
1690.00748
170.112
180.134
190.12
20.787
200.199
210.1
220.182
230.25
240.0663
250.51
264.05408e-4
270.646
280.728
290.018
30.0569
300.869
310.776
320.0294
330.0699
340.649
350.638
360.12
370.0347
380.273
390.306
40.714
400.0295
410.318
420.278
430.112
440.231
450.646
460.0657
470.0666
480.0569
490.148
50.365
500.345
510.386
520.438
530.952
540.348
550.467
560.489
570.264
580.288
590.0723
60.907
600.0553
610.129
620.166
630.151
640.157
650.187
660.125
670.336
680.195
690.32
70.0659
700.0431
710.0118
720.4
730.0348
740.596
750.0394
760.468
770.152
780.00133
790.219
80.0761
800.651
810.562
820.428
830.0876
840.843
850.153
860.217
879.8541e-4
880.775
890.377
90.415
900.0499
910.324
920.361
930.945
940.133
950.0263
960.811
970.729
980.179
990.43



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: CNhs12321


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)
0001873 (caudate nucleus)
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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