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FF:10167-103B5: 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:amygdala - 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
tissueamygdala
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-Neural0.466
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-penis0.735
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-0.354
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs13793

Jaspar motifP-value
MA0002.20.043
MA0003.10.331
MA0004.10.269
MA0006.10.212
MA0007.10.247
MA0009.10.338
MA0014.10.536
MA0017.10.00695
MA0018.20.13
MA0019.10.623
MA0024.10.459
MA0025.10.668
MA0027.10.357
MA0028.10.0199
MA0029.10.0864
MA0030.10.659
MA0031.10.496
MA0035.20.0125
MA0038.10.592
MA0039.20.0557
MA0040.10.535
MA0041.10.974
MA0042.10.974
MA0043.10.785
MA0046.10.0076
MA0047.20.0391
MA0048.10.0844
MA0050.11.38879e-4
MA0051.10.00316
MA0052.10.523
MA0055.10.00131
MA0057.10.978
MA0058.10.155
MA0059.10.0971
MA0060.10.658
MA0061.10.0113
MA0062.21.53352e-4
MA0065.20.00161
MA0066.10.0727
MA0067.10.699
MA0068.10.528
MA0069.10.561
MA0070.10.75
MA0071.10.0292
MA0072.10.243
MA0073.10.323
MA0074.10.154
MA0076.10.051
MA0077.10.89
MA0078.10.775
MA0079.20.957
MA0080.21.62532e-9
MA0081.10.0285
MA0083.10.0415
MA0084.10.801
MA0087.10.578
MA0088.10.148
MA0090.10.277
MA0091.10.855
MA0092.10.486
MA0093.10.247
MA0099.25.1366e-18
MA0100.10.581
MA0101.10.00179
MA0102.20.225
MA0103.10.334
MA0104.20.566
MA0105.10.0114
MA0106.10.0282
MA0107.10.00354
MA0108.20.763
MA0111.10.495
MA0112.20.00169
MA0113.10.625
MA0114.10.00282
MA0115.10.582
MA0116.10.0243
MA0117.10.961
MA0119.10.1
MA0122.10.566
MA0124.10.709
MA0125.10.41
MA0131.10.831
MA0135.10.0328
MA0136.13.58508e-14
MA0137.20.778
MA0138.20.144
MA0139.10.424
MA0140.15.23344e-4
MA0141.10.0124
MA0142.10.444
MA0143.10.558
MA0144.10.306
MA0145.10.188
MA0146.10.00339
MA0147.10.463
MA0148.10.0163
MA0149.10.0382
MA0150.11.55277e-4
MA0152.10.539
MA0153.10.351
MA0154.10.0977
MA0155.10.549
MA0156.11.93248e-10
MA0157.10.418
MA0159.10.0143
MA0160.10.00934
MA0162.10.127
MA0163.12.48495e-4
MA0164.10.867
MA0258.10.0121
MA0259.10.919



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: CNhs13793

Novel motifP-value
10.0751
100.0333
1000.257
1010.279
1020.756
1030.19
1040.121
1050.144
1060.034
1070.102
1080.853
1090.00233
110.015
1100.0603
1110.383
1120.495
1130.443
1140.464
1150.88
1160.123
1170.0059
1180.122
1190.196
120.506
1200.256
1210.348
1220.652
1230.829
1240.0164
1250.512
1260.0295
1270.451
1280.22
1290.594
133.23748e-4
1300.0758
1310.0772
1320.591
1330.00155
1340.579
1350.115
1367.11523e-4
1370.781
1380.853
1390.309
140.811
1400.407
1410.586
1420.749
1430.106
1440.81
1450.141
1460.292
1470.741
1480.476
1490.242
150.0949
1500.14
1510.532
1520.0442
1530.848
1540.343
1550.623
1560.816
1570.408
1580.435
1590.0474
160.0769
1600.321
1610.198
1620.968
1630.46
1640.0256
1650.0332
1660.424
1670.799
1680.45
1690.0138
170.122
180.229
190.172
20.795
200.0907
210.0715
220.143
230.5
240.0243
250.507
261.20523e-5
270.863
280.685
290.0149
30.0351
300.819
310.882
320.0355
330.0583
340.559
350.775
360.215
370.0376
380.425
390.208
40.873
400.0387
410.516
420.212
430.0955
440.272
450.671
460.131
470.0967
480.0399
490.183
50.549
500.151
510.491
520.46
530.862
540.336
550.353
560.409
570.332
580.436
590.069
60.846
600.0384
610.0411
620.364
630.134
640.305
650.356
660.096
670.242
680.0652
690.539
70.0278
700.136
710.00969
720.298
730.0176
740.801
750.021
760.438
770.164
780.00124
790.388
80.0956
800.577
810.881
820.694
830.0106
840.399
850.285
860.143
871.61448e-4
880.748
890.954
90.398
900.0669
910.769
920.988
930.649
940.395
950.0117
960.996
970.689
980.533
990.617



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: CNhs13793


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)
0000349 (limbic system)
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)
0001876 (amygdala)
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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