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FF:10196-103E7: 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:ductus deferens, 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
sex24
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 numberR1234100-10
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-penis0.332
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-0.394
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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: CNhs12846

Jaspar motifP-value
MA0002.20.0232
MA0003.10.691
MA0004.10.0779
MA0006.10.308
MA0007.10.711
MA0009.10.303
MA0014.10.753
MA0017.10.0576
MA0018.20.181
MA0019.10.0883
MA0024.10.0456
MA0025.10.268
MA0027.10.857
MA0028.10.0216
MA0029.10.625
MA0030.10.0377
MA0031.10.181
MA0035.20.693
MA0038.10.248
MA0039.20.936
MA0040.10.605
MA0041.10.383
MA0042.10.528
MA0043.10.0189
MA0046.15.15425e-4
MA0047.20.945
MA0048.10.125
MA0050.10.11
MA0051.10.0475
MA0052.10.861
MA0055.10.044
MA0057.10.952
MA0058.10.0229
MA0059.14.52411e-4
MA0060.10.636
MA0061.13.33255e-6
MA0062.21.98228e-4
MA0065.20.0277
MA0066.10.00316
MA0067.10.00518
MA0068.10.765
MA0069.10.724
MA0070.10.317
MA0071.10.17
MA0072.10.312
MA0073.10.42
MA0074.10.648
MA0076.10.00815
MA0077.10.685
MA0078.10.116
MA0079.20.331
MA0080.22.52783e-4
MA0081.10.00616
MA0083.10.0103
MA0084.10.481
MA0087.10.0926
MA0088.10.173
MA0090.10.346
MA0091.10.036
MA0092.10.799
MA0093.10.0878
MA0099.24.71518e-21
MA0100.10.0965
MA0101.16.97671e-7
MA0102.20.107
MA0103.10.12
MA0104.28.05149e-4
MA0105.11.85838e-10
MA0106.10.0598
MA0107.14.54386e-7
MA0108.20.0413
MA0111.10.281
MA0112.20.0382
MA0113.10.0816
MA0114.10.00726
MA0115.10.263
MA0116.13.77621e-6
MA0117.10.139
MA0119.10.83
MA0122.10.986
MA0124.10.62
MA0125.10.725
MA0131.10.718
MA0135.10.564
MA0136.13.14639e-4
MA0137.20.567
MA0138.20.86
MA0139.10.291
MA0140.10.211
MA0141.10.0675
MA0142.10.342
MA0143.10.386
MA0144.10.984
MA0145.10.539
MA0146.10.826
MA0147.13.632e-4
MA0148.10.838
MA0149.10.0832
MA0150.11.06882e-4
MA0152.10.595
MA0153.11.24466e-5
MA0154.10.00158
MA0155.10.887
MA0156.12.51647e-6
MA0157.10.578
MA0159.10.348
MA0160.10.717
MA0162.10.276
MA0163.11.35931e-9
MA0164.10.471
MA0258.10.481
MA0259.10.0662



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: CNhs12846

Novel motifP-value
10.0999
100.125
1000.461
1010.76
1020.955
1030.289
1040.467
1050.0271
1060.248
1070.538
1080.816
1090.0114
110.0282
1100.0346
1110.181
1120.548
1130.577
1140.342
1150.992
1160.804
1170.0418
1180.281
1190.669
120.729
1200.0211
1210.806
1220.903
1230.847
1240.204
1250.254
1260.537
1270.413
1280.592
1290.641
130.259
1300.211
1310.934
1320.0299
1330.248
1340.996
1350.845
1360.684
1370.0708
1380.538
1390.505
140.869
1400.713
1410.368
1420.524
1430.0352
1440.914
1450.972
1460.455
1470.365
1480.39
1490.65
150.0202
1500.5
1510.67
1520.591
1530.873
1540.835
1550.796
1560.579
1570.174
1580.621
1590.0191
160.381
1600.248
1610.628
1620.988
1630.887
1640.101
1650.8
1660.923
1670.714
1680.153
1690.579
170.162
180.0086
190.612
20.225
200.304
210.868
220.727
230.759
240.306
250.157
260.0628
270.543
280.646
290.0224
30.0901
300.248
310.864
320.642
330.114
340.812
350.254
360.00974
370.168
380.723
390.696
40.139
400.0197
418.46895e-4
420.0923
430.12
440.666
450.916
460.033
470.022
480.186
490.162
50.201
500.597
510.151
520.204
530.666
540.358
550.761
560.716
570.37
580.479
590.134
60.323
600.568
610.377
620.102
630.475
640.219
650.48
660.0967
670.392
681
690.658
70.116
700.39
710.0646
720.35
730.0697
740.346
750.0187
760.0618
770.38
780.44
790.301
80.2
800.0293
810.682
820.723
830.805
840.949
850.309
860.382
870.0169
880.869
890.117
90.555
900.239
910.553
920.894
930.0579
940.0967
951.3681e-4
960.531
970.407
980.489
990.7



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: CNhs12846


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
0000058 (duct)
0000061 (anatomical structure)
0000062 (organ)
0000079 (male reproductive system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0001000 (vas deferens)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003101 (male organism)
0003133 (reproductive organ)
0003135 (male reproductive organ)
0004054 (internal male genitalia)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004175 (internal genitalia)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005904 (duct of male reproductive system)
0006947 (male genital duct)
0007023 (adult organism)

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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