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FF:10037-101F1: 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 16:29, 29 March 2012


Name:nucleus accumbens, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuenucleus accumbens
dev stage23-56 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number6070307
catalog numberCat:636569
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-Neural0.346
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-penis0.155
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-0.333
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0525
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs10644

Jaspar motifP-value
MA0002.20.0106
MA0003.10.358
MA0004.10.469
MA0006.10.369
MA0007.10.215
MA0009.10.212
MA0014.10.687
MA0017.10.0031
MA0018.20.0738
MA0019.10.791
MA0024.10.988
MA0025.10.184
MA0027.10.406
MA0028.10.133
MA0029.10.0541
MA0030.10.193
MA0031.10.972
MA0035.20.128
MA0038.10.0357
MA0039.20.293
MA0040.10.558
MA0041.10.226
MA0042.10.624
MA0043.10.321
MA0046.10.0986
MA0047.20.132
MA0048.10.118
MA0050.10.018
MA0051.10.141
MA0052.10.119
MA0055.10.00286
MA0057.10.944
MA0058.10.434
MA0059.10.0813
MA0060.10.194
MA0061.10.00975
MA0062.20.0351
MA0065.24.9768e-4
MA0066.10.0236
MA0067.10.648
MA0068.10.361
MA0069.10.542
MA0070.10.099
MA0071.10.0255
MA0072.10.418
MA0073.10.37
MA0074.10.211
MA0076.10.328
MA0077.10.28
MA0078.10.793
MA0079.20.376
MA0080.23.85317e-8
MA0081.10.0651
MA0083.10.164
MA0084.10.481
MA0087.10.347
MA0088.10.135
MA0090.10.251
MA0091.10.382
MA0092.10.331
MA0093.10.507
MA0099.27.97974e-11
MA0100.10.841
MA0101.10.00927
MA0102.20.205
MA0103.10.227
MA0104.20.45
MA0105.15.466e-4
MA0106.10.0278
MA0107.10.0124
MA0108.20.341
MA0111.10.442
MA0112.27.95935e-4
MA0113.10.335
MA0114.10.0031
MA0115.10.304
MA0116.10.00374
MA0117.10.912
MA0119.10.0473
MA0122.10.957
MA0124.10.581
MA0125.10.172
MA0131.10.921
MA0135.10.0118
MA0136.16.82446e-10
MA0137.20.62
MA0138.20.285
MA0139.10.378
MA0140.10.0176
MA0141.10.0109
MA0142.10.901
MA0143.10.702
MA0144.10.337
MA0145.10.216
MA0146.10.012
MA0147.10.318
MA0148.10.126
MA0149.10.011
MA0150.10.00183
MA0152.10.865
MA0153.10.637
MA0154.10.035
MA0155.10.701
MA0156.14.90092e-5
MA0157.10.545
MA0159.10.00771
MA0160.10.0339
MA0162.10.109
MA0163.11.73581e-6
MA0164.10.673
MA0258.10.00992
MA0259.10.779



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: CNhs10644

Novel motifP-value
10.0299
100.0264
1000.26
1010.717
1020.818
1030.209
1040.163
1050.372
1060.0516
1070.126
1080.771
1090.00923
110.0136
1100.0458
1110.0536
1120.351
1130.658
1140.0847
1150.951
1160.159
1170.00991
1180.12
1190.0902
120.838
1200.13
1210.646
1220.564
1230.41
1240.072
1250.177
1260.0343
1270.466
1280.157
1290.543
130.00207
1300.679
1310.0397
1320.732
1330.0012
1340.296
1350.192
1360.0133
1370.751
1380.818
1390.0777
140.883
1400.0974
1410.185
1420.772
1430.0109
1440.816
1450.0964
1460.585
1470.926
1480.0932
1490.332
150.0805
1500.178
1510.595
1520.125
1530.736
1540.576
1550.354
1560.492
1570.494
1580.755
1590.0533
160.0659
1600.184
1610.254
1620.942
1630.991
1640.0185
1650.0374
1660.86
1670.283
1680.621
1690.00686
170.151
180.178
190.175
20.984
200.0864
210.0868
220.242
230.432
240.136
250.479
261.99153e-4
270.888
280.723
290.0121
30.0287
300.575
310.86
320.0261
330.0732
340.803
350.483
360.0835
370.0345
380.313
390.271
40.889
400.0465
410.458
420.193
430.104
440.0872
450.805
460.0534
470.0576
480.0545
490.12
50.437
500.368
510.51
520.658
530.954
540.467
550.349
560.484
570.23
580.29
590.121
60.569
600.0831
610.0874
620.168
630.158
640.173
650.26
660.271
670.329
680.395
690.28
70.0696
700.0142
710.0102
720.449
730.0419
740.525
750.0266
760.36
770.188
780.002
790.134
80.0503
800.976
810.502
820.387
830.219
840.713
850.182
860.203
870.00611
880.843
890.497
90.545
900.0365
910.309
920.4
930.784
940.0575
950.031
960.9
970.778
980.173
990.635



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: CNhs10644


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)
0001882 (nucleus accumbens)
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)
0005403 (ventral striatum)
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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