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FF:10200-103F2: 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 17:26, 29 March 2012


Name:penis, adult
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sex29
ageM
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberR1234194-50
sample typeNA
extraction protocol (Details)NA
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
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-penis0.549
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-0.308
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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: CNhs12850

Jaspar motifP-value
MA0002.20.00207
MA0003.10.191
MA0004.10.00111
MA0006.10.237
MA0007.10.731
MA0009.10.471
MA0014.10.18
MA0017.10.72
MA0018.27.08182e-4
MA0019.10.327
MA0024.10.00365
MA0025.10.0767
MA0027.10.682
MA0028.14.65241e-12
MA0029.10.395
MA0030.10.942
MA0031.10.996
MA0035.20.0164
MA0038.19.3689e-4
MA0039.20.00412
MA0040.10.162
MA0041.10.616
MA0042.10.721
MA0043.14.25891e-6
MA0046.10.00242
MA0047.20.952
MA0048.10.0205
MA0050.10.119
MA0051.10.0583
MA0052.15.62318e-15
MA0055.11.06225e-4
MA0057.10.484
MA0058.15.92645e-5
MA0059.12.19757e-4
MA0060.12.76527e-12
MA0061.16.62717e-6
MA0062.21.45269e-19
MA0065.20.723
MA0066.10.317
MA0067.10.00663
MA0068.10.999
MA0069.10.31
MA0070.10.162
MA0071.10.94
MA0072.10.238
MA0073.10.758
MA0074.10.467
MA0076.11.18672e-13
MA0077.10.144
MA0078.10.462
MA0079.20.997
MA0080.29.90333e-7
MA0081.10.00738
MA0083.11.2164e-4
MA0084.10.931
MA0087.10.85
MA0088.10.0502
MA0090.10.293
MA0091.10.243
MA0092.10.222
MA0093.14.57695e-4
MA0099.21.41045e-22
MA0100.10.00278
MA0101.15.95194e-7
MA0102.20.00171
MA0103.10.391
MA0104.24.76039e-6
MA0105.10.0029
MA0106.10.196
MA0107.11.06253e-7
MA0108.21.31603e-8
MA0111.10.991
MA0112.20.0149
MA0113.10.0422
MA0114.10.256
MA0115.10.987
MA0116.10.156
MA0117.10.15
MA0119.10.138
MA0122.10.397
MA0124.10.799
MA0125.10.774
MA0131.10.0459
MA0135.10.618
MA0136.13.40988e-11
MA0137.20.108
MA0138.20.0387
MA0139.10.0784
MA0140.10.00115
MA0141.10.877
MA0142.10.0609
MA0143.10.449
MA0144.10.32
MA0145.10.0842
MA0146.10.164
MA0147.13.82194e-6
MA0148.10.962
MA0149.10.0866
MA0150.13.57868e-6
MA0152.10.382
MA0153.10.848
MA0154.10.788
MA0155.10.179
MA0156.18.5815e-15
MA0157.10.675
MA0159.10.774
MA0160.10.541
MA0162.10.176
MA0163.10.0908
MA0164.10.665
MA0258.10.0479
MA0259.10.0042



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: CNhs12850

Novel motifP-value
10.648
100.282
1000.31
1010.513
1020.513
1030.494
1040.681
1050.459
1060.156
1070.0154
1080.0811
1090.0521
110.527
1100.697
1110.848
1120.135
1130.702
1140.862
1150.00609
1160.0279
1170.0648
1180.0219
1190.0782
120.475
1200.241
1210.546
1220.228
1230.631
1240.194
1250.862
1260.494
1270.798
1280.023
1290.94
130.28
1300.398
1310.416
1320.0107
1330.00402
1340.221
1350.0575
1360.0594
1370.729
1380.42
1390.0953
140.745
1400.665
1410.78
1420.597
1430.17
1440.686
1450.868
1460.557
1470.014
1480.739
1490.212
150.133
1500.904
1510.607
1520.576
1530.24
1540.892
1550.6
1560.755
1570.55
1580.512
1590.182
160.593
1600.537
1610.434
1620.635
1630.279
1640.566
1650.0636
1660.0801
1670.339
1680.817
1690.0982
170.919
180.449
190.00899
20.00312
200.0212
210.444
220.57
230.146
240.185
250.628
260.399
270.792
280.469
290.0751
30.753
300.046
310.416
320.079
330.234
340.317
350.871
360.0205
370.969
380.898
390.186
40.364
400.0269
410.134
420.335
430.735
440.0154
450.142
460.9
470.384
480.371
490.774
50.709
500.595
510.489
520.0911
530.888
540.782
550.946
560.892
570.802
580.963
590.233
60.509
600.287
610.375
620.747
630.388
640.48
650.323
662.60753e-4
670.986
680.242
690.305
70.578
700.793
710.429
720.638
730.263
740.493
750.143
760.0893
770.0168
780.81
790.0447
80.799
800.305
810.294
820.14
830.78
840.879
850.0241
860.596
870.0141
880.762
890.0455
90.829
900.445
910.0573
920.202
930.285
940.132
950.00303
960.681
970.675
980.365
990.0285



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: CNhs12850


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
0000061 (anatomical structure)
0000062 (organ)
0000079 (male reproductive system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000989 (penis)
0000990 (reproductive system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003064 (intermediate mesoderm)
0003081 (lateral plate mesoderm)
0003101 (male organism)
0003104 (mesenchyme)
0003133 (reproductive organ)
0003135 (male reproductive organ)
0004120 (mesoderm-derived structure)
0004874 (somatopleure)
0004876 (urogenital ridge)
0005156 (reproductive structure)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005876 (undifferentiated genital tubercle)
0006258 (lateral plate mesenchyme)
0007023 (adult organism)
0008811 (intromittent organ)
0009142 (entire embryonic mesenchyme)

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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