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FF:10166-103B4: 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:cerebellum, 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
tissuecerebellum
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-Neural0.191
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-penis0.676
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
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: CNhs12323

Jaspar motifP-value
MA0002.20.0162
MA0003.10.171
MA0004.10.335
MA0006.10.239
MA0007.10.319
MA0009.10.334
MA0014.10.599
MA0017.10.0013
MA0018.20.212
MA0019.10.641
MA0024.10.431
MA0025.10.248
MA0027.10.84
MA0028.10.146
MA0029.10.0881
MA0030.10.185
MA0031.10.247
MA0035.20.0187
MA0038.10.3
MA0039.20.235
MA0040.10.818
MA0041.10.532
MA0042.10.971
MA0043.10.837
MA0046.10.038
MA0047.20.103
MA0048.10.37
MA0050.10.0135
MA0051.10.0316
MA0052.10.435
MA0055.10.0432
MA0057.10.437
MA0058.10.316
MA0059.10.0602
MA0060.10.0395
MA0061.10.0078
MA0062.20.0091
MA0065.24.53477e-4
MA0066.10.0118
MA0067.10.903
MA0068.10.68
MA0069.10.971
MA0070.10.699
MA0071.10.154
MA0072.10.89
MA0073.10.333
MA0074.10.21
MA0076.10.248
MA0077.10.449
MA0078.10.531
MA0079.20.804
MA0080.23.84216e-9
MA0081.10.0679
MA0083.10.00429
MA0084.10.561
MA0087.10.878
MA0088.10.366
MA0090.10.211
MA0091.10.861
MA0092.10.233
MA0093.10.365
MA0099.21.4775e-17
MA0100.10.633
MA0101.10.00491
MA0102.20.102
MA0103.10.44
MA0104.20.544
MA0105.10.00225
MA0106.10.025
MA0107.10.00418
MA0108.20.114
MA0111.10.486
MA0112.20.00155
MA0113.10.485
MA0114.10.00282
MA0115.10.448
MA0116.10.00789
MA0117.10.856
MA0119.10.175
MA0122.10.457
MA0124.10.982
MA0125.10.526
MA0131.10.648
MA0135.10.41
MA0136.11.24622e-12
MA0137.20.763
MA0138.20.453
MA0139.10.619
MA0140.10.00329
MA0141.10.00314
MA0142.10.962
MA0143.10.766
MA0144.10.336
MA0145.10.126
MA0146.10.0558
MA0147.10.367
MA0148.10.0872
MA0149.10.0286
MA0150.15.48103e-4
MA0152.10.305
MA0153.10.177
MA0154.10.032
MA0155.10.321
MA0156.12.2013e-7
MA0157.10.949
MA0159.10.00288
MA0160.10.0229
MA0162.10.098
MA0163.13.04699e-5
MA0164.10.942
MA0258.10.0184
MA0259.10.849



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: CNhs12323

Novel motifP-value
10.0506
100.0776
1000.482
1010.814
1020.608
1030.0604
1040.123
1050.163
1060.0111
1070.0395
1080.717
1090.00233
110.0179
1100.0581
1110.362
1120.372
1130.366
1140.188
1150.994
1160.207
1170.0165
1180.274
1190.298
120.748
1200.156
1210.673
1220.904
1230.304
1240.381
1250.292
1260.0459
1270.389
1280.148
1290.435
130.00412
1300.155
1310.288
1320.738
1330.372
1340.501
1350.703
1360.00277
1370.558
1380.825
1390.118
140.71
1400.754
1410.575
1420.795
1430.0624
1440.959
1450.226
1460.537
1470.901
1480.0195
1490.0737
150.0936
1500.223
1510.65
1520.0306
1530.982
1540.624
1550.516
1560.579
1570.353
1580.0409
1590.00616
160.0597
1600.215
1610.298
1620.768
1630.828
1640.0852
1650.0763
1660.703
1670.888
1680.322
1690.0197
170.0887
180.141
190.234
20.77
200.318
210.0707
220.202
230.164
240.0504
250.499
260.00113
270.494
280.767
290.0218
30.0559
300.923
310.897
320.0486
330.0604
340.554
350.763
360.202
370.0412
380.345
390.169
40.849
400.0493
410.224
420.243
430.113
440.182
450.652
460.0556
470.0535
480.0919
490.271
50.463
500.359
510.4
520.294
530.848
540.387
550.616
560.362
570.367
580.344
590.0396
60.959
600.0353
610.0734
620.147
630.136
640.29
650.225
660.272
670.43
680.164
690.355
70.0619
700.0165
710.0131
720.313
730.0187
740.84
750.0573
760.486
770.103
780.0308
790.349
80.0311
800.198
810.421
820.478
830.0259
840.697
850.121
860.246
872.3479e-4
880.83
890.19
90.33
900.0782
910.773
920.391
930.942
940.186
950.012
960.883
970.665
980.379
990.407



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: CNhs12323


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)
0000063 (organ segment)
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)
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)
0001895 (metencephalon)
0002028 (hindbrain)
0002037 (cerebellum)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002680 (regional part of metencephalon)
0003057 (chordal neural plate)
0003075 (neural plate)
0003076 (posterior neural tube)
0004121 (ectoderm-derived structure)
0004732 (segmental subdivision of nervous system)
0004733 (segmental subdivision of hindbrain)
0005068 (neural rod)
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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