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FF:10032-101E5: 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 16:28, 29 March 2012


Name:postcentral gyrus, 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
tissuepostcentral gyrus
dev stage44-52 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 number3040377
catalog numberCat:636573
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-Neural0.312
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-penis0.161
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-0.392
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0537
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: CNhs10638

Jaspar motifP-value
MA0002.20.00727
MA0003.10.41
MA0004.10.483
MA0006.10.399
MA0007.10.212
MA0009.10.165
MA0014.10.62
MA0017.10.00461
MA0018.20.0395
MA0019.10.802
MA0024.10.902
MA0025.10.148
MA0027.10.62
MA0028.10.074
MA0029.10.15
MA0030.10.217
MA0031.10.991
MA0035.20.126
MA0038.10.0511
MA0039.20.192
MA0040.10.406
MA0041.10.171
MA0042.10.652
MA0043.10.312
MA0046.10.143
MA0047.20.0523
MA0048.10.0877
MA0050.10.00131
MA0051.10.0597
MA0052.10.0587
MA0055.10.00204
MA0057.10.999
MA0058.10.437
MA0059.10.0855
MA0060.10.227
MA0061.10.00793
MA0062.20.0126
MA0065.28.88493e-4
MA0066.10.0406
MA0067.10.722
MA0068.10.153
MA0069.10.499
MA0070.10.0459
MA0071.10.0456
MA0072.10.526
MA0073.10.436
MA0074.10.196
MA0076.10.183
MA0077.10.17
MA0078.10.94
MA0079.20.373
MA0080.22.64965e-8
MA0081.10.04
MA0083.10.144
MA0084.10.688
MA0087.10.364
MA0088.10.141
MA0090.10.217
MA0091.10.548
MA0092.10.424
MA0093.10.512
MA0099.21.16641e-10
MA0100.10.518
MA0101.10.00284
MA0102.20.096
MA0103.10.299
MA0104.20.44
MA0105.14.58267e-4
MA0106.10.0326
MA0107.10.00579
MA0108.20.235
MA0111.10.419
MA0112.20.0013
MA0113.10.254
MA0114.10.00376
MA0115.10.428
MA0116.10.00275
MA0117.10.93
MA0119.10.0373
MA0122.10.756
MA0124.10.744
MA0125.10.245
MA0131.10.853
MA0135.10.00687
MA0136.12.19669e-10
MA0137.20.258
MA0138.20.0965
MA0139.10.403
MA0140.10.011
MA0141.10.028
MA0142.10.995
MA0143.10.902
MA0144.10.219
MA0145.10.251
MA0146.10.0122
MA0147.10.311
MA0148.10.0639
MA0149.10.0163
MA0150.10.00184
MA0152.10.797
MA0153.10.333
MA0154.10.0444
MA0155.10.769
MA0156.15.43349e-6
MA0157.10.635
MA0159.10.00701
MA0160.10.0523
MA0162.10.134
MA0163.12.86263e-6
MA0164.10.783
MA0258.10.0151
MA0259.10.74



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: CNhs10638

Novel motifP-value
10.033
100.0217
1000.297
1010.924
1020.701
1030.178
1040.17
1050.338
1060.0712
1070.127
1080.889
1090.0102
110.016
1100.0355
1110.0609
1120.328
1130.675
1140.0721
1150.971
1160.217
1170.0079
1180.0873
1190.111
120.795
1200.141
1210.662
1220.551
1230.785
1240.0252
1250.156
1260.0221
1270.484
1280.18
1290.628
137.57082e-4
1300.474
1310.0774
1320.697
1330.00139
1340.258
1350.135
1360.00964
1370.708
1380.791
1390.0849
140.937
1400.118
1410.23
1420.945
1430.0104
1440.848
1450.102
1460.649
1470.939
1480.151
1490.376
150.0658
1500.162
1510.706
1520.156
1530.63
1540.585
1550.357
1560.44
1570.355
1580.877
1590.139
160.0752
1600.222
1610.163
1620.882
1630.737
1640.0159
1650.0205
1660.811
1670.266
1680.692
1690.00764
170.187
180.214
190.217
20.933
200.0729
210.0873
220.263
230.429
240.11
250.443
264.21253e-5
270.957
280.603
290.00821
30.0228
300.532
310.95
320.035
330.0684
340.859
350.52
360.1
370.0421
380.327
390.261
40.986
400.0664
410.464
420.152
430.105
440.0855
450.855
460.0487
470.0644
480.0583
490.138
50.431
500.36
510.561
520.653
530.891
540.515
550.3
560.502
570.246
580.281
590.172
60.58
600.0745
610.0561
620.158
630.177
640.231
650.323
660.277
670.358
680.36
690.479
70.0501
700.0228
710.00724
720.486
730.047
740.487
750.0272
760.333
770.29
780.00224
790.171
80.0562
800.939
810.59
820.486
830.188
840.694
850.309
860.197
870.0125
880.841
890.613
90.548
900.0345
910.348
920.44
930.791
940.0652
950.0272
960.948
970.761
980.224
990.94



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: CNhs10638


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)
0000153 (anterior region of body)
0000200 (gyrus)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0000956 (cerebral cortex)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001872 (parietal lobe)
0001890 (forebrain)
0001893 (telencephalon)
0001950 (neocortex)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002581 (postcentral gyrus)
0002616 (regional part of brain)
0002619 (regional part of cerebral cortex)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
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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