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FF:10175-103C4: 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 17:39, 29 March 2012


Name:globus pallidus - 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
tissueglobus pallidus
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-Neural0.204
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-penis0.636
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-0.342
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs13801

Jaspar motifP-value
MA0002.20.0443
MA0003.10.283
MA0004.10.336
MA0006.10.341
MA0007.10.784
MA0009.10.197
MA0014.10.73
MA0017.10.0175
MA0018.20.0528
MA0019.10.803
MA0024.10.819
MA0025.10.273
MA0027.10.362
MA0028.10.0704
MA0029.10.0731
MA0030.10.204
MA0031.10.769
MA0035.20.0594
MA0038.10.134
MA0039.20.218
MA0040.10.712
MA0041.10.488
MA0042.10.43
MA0043.10.349
MA0046.10.0199
MA0047.20.311
MA0048.10.0788
MA0050.10.0632
MA0051.10.23
MA0052.10.407
MA0055.10.00102
MA0057.10.912
MA0058.10.399
MA0059.10.103
MA0060.10.391
MA0061.10.0043
MA0062.20.00279
MA0065.20.00354
MA0066.10.0187
MA0067.10.444
MA0068.10.442
MA0069.10.886
MA0070.10.374
MA0071.10.0172
MA0072.10.611
MA0073.10.42
MA0074.10.246
MA0076.10.115
MA0077.10.00314
MA0078.10.318
MA0079.20.834
MA0080.25.22509e-8
MA0081.10.0186
MA0083.10.118
MA0084.10.129
MA0087.10.122
MA0088.10.151
MA0090.10.159
MA0091.10.488
MA0092.10.361
MA0093.10.372
MA0099.23.30317e-16
MA0100.10.418
MA0101.10.00454
MA0102.20.237
MA0103.10.0935
MA0104.20.462
MA0105.13.49989e-4
MA0106.10.0358
MA0107.10.00446
MA0108.20.676
MA0111.10.672
MA0112.20.00137
MA0113.10.617
MA0114.10.0131
MA0115.10.962
MA0116.10.00389
MA0117.10.81
MA0119.10.102
MA0122.10.51
MA0124.10.855
MA0125.10.135
MA0131.10.813
MA0135.10.00679
MA0136.14.4499e-12
MA0137.20.0173
MA0138.20.297
MA0139.10.357
MA0140.10.0355
MA0141.10.0181
MA0142.10.452
MA0143.10.078
MA0144.10.957
MA0145.10.328
MA0146.10.00812
MA0147.10.335
MA0148.10.307
MA0149.10.0356
MA0150.15.37709e-4
MA0152.10.891
MA0153.10.566
MA0154.10.0389
MA0155.10.711
MA0156.11.45394e-7
MA0157.10.651
MA0159.10.0356
MA0160.10.0924
MA0162.10.155
MA0163.13.82954e-7
MA0164.10.848
MA0258.10.0224
MA0259.10.876



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: CNhs13801

Novel motifP-value
10.0574
100.0323
1000.287
1010.646
1020.803
1030.0592
1040.0463
1050.12
1060.0271
1070.158
1080.932
1090.00337
110.012
1100.0524
1110.233
1120.426
1130.353
1140.252
1150.606
1160.0889
1170.00539
1180.192
1190.198
120.545
1200.109
1210.3
1220.769
1230.803
1240.155
1250.631
1260.0937
1270.502
1280.237
1290.631
130.00233
1300.18
1310.00901
1320.58
1334.34902e-4
1340.809
1350.0868
1360.00438
1370.662
1380.859
1390.219
140.883
1400.841
1410.34
1420.969
1430.0224
1440.918
1450.262
1460.492
1470.731
1480.556
1490.235
150.0721
1500.138
1510.658
1520.0757
1530.911
1540.275
1550.633
1560.858
1570.546
1580.272
1590.033
160.043
1600.285
1610.166
1620.733
1630.621
1640.00435
1650.054
1660.843
1670.817
1680.446
1690.0139
170.111
180.0834
190.279
20.842
200.0842
210.0491
220.202
230.556
240.0255
250.499
266.76e-4
270.849
280.872
290.00502
30.0252
300.832
310.836
320.0167
330.0711
340.7
350.575
360.272
370.0257
380.39
390.326
40.927
400.112
410.562
420.236
430.131
440.0754
450.741
460.0269
470.07
480.0315
490.227
50.994
500.359
510.438
520.703
530.821
540.426
550.578
560.548
570.306
580.345
590.0438
60.902
600.0896
610.0573
620.228
630.277
640.169
650.28
660.124
670.22
680.313
690.53
70.0965
700.0281
710.00963
720.317
730.0338
740.992
750.0102
760.287
770.12
780.00557
790.174
80.0571
800.6
810.458
820.753
830.0758
840.479
850.447
860.14
877.83453e-4
880.642
890.317
90.451
900.146
910.681
920.641
930.771
940.152
950.0265
960.872
970.763
980.173
990.491



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: CNhs13801


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)
0001875 (globus pallidus)
0001890 (forebrain)
0001893 (telencephalon)
0002020 (gray matter)
0002050 (embryonic structure)
0002308 (nucleus of brain)
0002346 (neurectoderm)
0002420 (basal ganglion)
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)
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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