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FF:10076-102A4: 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 16:53, 29 March 2012


Name:occipital lobe, adult, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueoccipital lobe
dev stage27 years old adult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA505663
catalog numberCat:RtpHAN: Brain
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-Neural0.422
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-penis0.145
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-0.356
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: CNhs11787

Jaspar motifP-value
MA0002.20.0049
MA0003.10.313
MA0004.10.356
MA0006.10.378
MA0007.10.263
MA0009.10.214
MA0014.10.537
MA0017.10.00284
MA0018.20.0673
MA0019.10.888
MA0024.10.901
MA0025.10.534
MA0027.10.761
MA0028.10.065
MA0029.10.0499
MA0030.10.665
MA0031.10.467
MA0035.20.0345
MA0038.10.306
MA0039.20.0702
MA0040.10.705
MA0041.10.828
MA0042.10.978
MA0043.10.561
MA0046.10.0157
MA0047.20.0397
MA0048.10.111
MA0050.14.67964e-4
MA0051.10.035
MA0052.10.662
MA0055.10.00162
MA0057.10.843
MA0058.10.276
MA0059.10.0875
MA0060.10.803
MA0061.10.00591
MA0062.20.00341
MA0065.24.72889e-4
MA0066.10.0271
MA0067.10.785
MA0068.10.0969
MA0069.10.442
MA0070.10.325
MA0071.10.027
MA0072.10.229
MA0073.10.322
MA0074.10.211
MA0076.10.11
MA0077.10.27
MA0078.10.753
MA0079.20.596
MA0080.21.07389e-9
MA0081.10.0205
MA0083.10.0591
MA0084.10.78
MA0087.10.695
MA0088.10.121
MA0090.10.236
MA0091.10.617
MA0092.10.353
MA0093.10.363
MA0099.21.18096e-17
MA0100.10.383
MA0101.19.57996e-4
MA0102.20.0568
MA0103.10.28
MA0104.20.411
MA0105.10.00109
MA0106.10.037
MA0107.10.00213
MA0108.20.564
MA0111.10.614
MA0112.26.78574e-4
MA0113.10.268
MA0114.10.00299
MA0115.10.449
MA0116.10.00485
MA0117.10.955
MA0119.10.0484
MA0122.10.769
MA0124.10.684
MA0125.10.376
MA0131.10.766
MA0135.10.097
MA0136.16.28882e-15
MA0137.20.313
MA0138.20.121
MA0139.10.423
MA0140.10.00696
MA0141.10.0169
MA0142.10.88
MA0143.10.872
MA0144.10.268
MA0145.10.2
MA0146.10.00695
MA0147.10.307
MA0148.10.0412
MA0149.10.0122
MA0150.12.59329e-4
MA0152.10.842
MA0153.10.136
MA0154.10.0378
MA0155.10.672
MA0156.14.37605e-9
MA0157.10.386
MA0159.10.00587
MA0160.10.0355
MA0162.10.16
MA0163.12.61642e-5
MA0164.10.958
MA0258.10.00896
MA0259.10.747



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: CNhs11787

Novel motifP-value
10.0512
100.0415
1000.331
1010.693
1020.768
1030.152
1040.116
1050.0985
1060.0945
1070.153
1080.786
1090.00674
110.0153
1100.036
1110.134
1120.619
1130.631
1140.097
1150.587
1160.297
1170.00903
1180.153
1190.19
120.517
1200.23
1210.393
1220.744
1230.787
1240.0783
1250.397
1260.0266
1270.381
1280.255
1290.58
134.87382e-4
1300.133
1310.208
1320.612
1330.00593
1340.534
1350.321
1360.0113
1370.66
1380.779
1390.153
140.692
1400.587
1410.339
1420.626
1430.0214
1440.989
1450.083
1460.386
1470.99
1480.381
1490.296
150.0736
1500.154
1510.649
1520.13
1530.765
1540.519
1550.369
1560.295
1570.424
1580.796
1590.189
160.0746
1600.223
1610.158
1620.696
1630.665
1640.027
1650.0535
1660.803
1670.52
1680.404
1690.0087
170.129
180.241
190.2
20.914
200.103
210.0949
220.194
230.413
240.0329
250.446
261.12338e-4
270.99
280.623
290.0121
30.0285
300.821
310.916
320.0403
330.0555
340.666
350.535
360.121
370.0353
380.276
390.248
40.878
400.0297
410.394
420.165
430.095
440.209
450.716
460.0672
470.0612
480.0503
490.127
50.487
500.232
510.472
520.617
530.984
540.407
550.422
560.475
570.35
580.288
590.147
60.77
600.0782
610.0598
620.173
630.152
640.237
650.284
660.132
670.315
680.306
690.495
70.0322
700.0556
710.00917
720.328
730.0385
740.571
750.0316
760.479
770.184
780.00284
790.476
80.096
800.545
810.691
820.718
830.0417
840.652
850.272
860.232
870.0036
880.864
890.55
90.403
900.0832
910.606
920.497
930.899
940.139
950.0213
960.82
970.718
980.194
990.734



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: CNhs11787


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)
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)
0000956 (cerebral cortex)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001890 (forebrain)
0001893 (telencephalon)
0001950 (neocortex)
0002021 (occipital lobe)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
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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