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FF:10201-103F3: 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:seminal vesicle, 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 numberR1234214-10
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-penis0.0322
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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: CNhs12851

Jaspar motifP-value
MA0002.20.0687
MA0003.10.388
MA0004.10.02
MA0006.10.0702
MA0007.10.582
MA0009.10.851
MA0014.10.265
MA0017.10.0428
MA0018.20.324
MA0019.10.163
MA0024.18.44882e-4
MA0025.10.174
MA0027.10.733
MA0028.12.06054e-5
MA0029.10.298
MA0030.10.142
MA0031.10.649
MA0035.20.238
MA0038.10.0176
MA0039.20.00937
MA0040.10.87
MA0041.10.269
MA0042.10.396
MA0043.10.02
MA0046.10.0619
MA0047.20.732
MA0048.10.0298
MA0050.10.17
MA0051.10.106
MA0052.10.959
MA0055.12.79614e-4
MA0057.10.959
MA0058.18.02065e-4
MA0059.17.81196e-4
MA0060.11.43109e-4
MA0061.13.24733e-6
MA0062.21.39999e-8
MA0065.20.104
MA0066.10.0324
MA0067.10.00141
MA0068.10.63
MA0069.10.256
MA0070.10.0778
MA0071.10.244
MA0072.10.191
MA0073.10.615
MA0074.10.236
MA0076.11.34959e-6
MA0077.10.765
MA0078.10.157
MA0079.20.771
MA0080.27.17591e-5
MA0081.17.94028e-4
MA0083.10.0347
MA0084.10.336
MA0087.10.223
MA0088.10.027
MA0090.10.351
MA0091.10.32
MA0092.10.753
MA0093.10.0182
MA0099.23.2776e-25
MA0100.10.01
MA0101.15.67529e-8
MA0102.20.0849
MA0103.10.00364
MA0104.21.64627e-5
MA0105.11.44671e-5
MA0106.10.102
MA0107.13.26028e-7
MA0108.20.11
MA0111.10.437
MA0112.20.598
MA0113.10.326
MA0114.10.00745
MA0115.10.433
MA0116.14.8953e-4
MA0117.10.438
MA0119.10.503
MA0122.10.956
MA0124.10.961
MA0125.10.341
MA0131.10.146
MA0135.10.271
MA0136.11.34262e-5
MA0137.20.222
MA0138.20.472
MA0139.10.854
MA0140.10.0363
MA0141.10.241
MA0142.10.479
MA0143.10.878
MA0144.10.919
MA0145.10.234
MA0146.10.746
MA0147.15.91815e-5
MA0148.10.611
MA0149.10.0828
MA0150.12.54216e-5
MA0152.10.557
MA0153.10.00218
MA0154.10.0115
MA0155.10.707
MA0156.11.61738e-8
MA0157.10.348
MA0159.10.894
MA0160.10.524
MA0162.10.897
MA0163.13.08835e-4
MA0164.10.588
MA0258.10.848
MA0259.10.0116



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: CNhs12851

Novel motifP-value
10.25
100.368
1000.508
1010.694
1020.934
1030.5
1040.688
1050.0556
1060.621
1070.415
1080.337
1090.023
110.127
1100.0262
1110.517
1120.314
1130.367
1140.969
1150.39
1160.446
1170.103
1180.608
1190.248
120.364
1200.0329
1210.831
1220.852
1230.395
1240.184
1250.696
1260.844
1270.207
1280.183
1290.832
130.223
1300.027
1310.678
1320.00839
1330.155
1340.837
1350.482
1360.873
1370.176
1380.406
1390.602
140.932
1400.935
1410.796
1420.601
1430.247
1440.528
1450.981
1460.409
1470.665
1480.75
1490.887
150.0658
1500.798
1510.816
1520.895
1530.631
1540.764
1550.707
1560.124
1570.29
1580.892
1590.0879
160.979
1600.459
1610.575
1620.417
1630.703
1640.109
1650.845
1660.251
1671
1680.417
1690.26
170.888
180.0444
190.115
20.00904
200.149
210.597
220.891
230.737
240.272
250.141
260.379
270.988
280.717
290.0663
30.174
300.112
310.744
320.0767
330.13
340.986
350.792
360.00832
370.378
380.744
390.319
40.126
400.0183
410.00232
420.0586
430.338
440.961
450.657
460.144
470.242
480.365
490.252
50.214
500.431
510.287
520.0559
530.473
540.541
550.382
560.841
570.747
580.894
590.548
60.493
600.943
610.558
620.491
630.998
640.358
650.803
660.0131
670.609
680.869
690.561
70.109
700.727
710.551
720.31
730.0679
740.383
750.0975
760.12
770.121
780.842
790.773
80.975
800.0136
810.859
820.531
830.972
840.934
850.689
860.798
870.12
880.94
890.458
90.485
900.865
910.407
920.391
930.0605
940.0946
951.67385e-5
960.302
970.513
980.541
990.489



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: CNhs12851


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)
0000080 (mesonephros)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000473 (testis)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000489 (cavitated compound organ)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000991 (gonad)
0000998 (seminal vesicle)
0001008 (renal system)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002100 (trunk)
0002113 (kidney)
0002120 (pronephros)
0002323 (body cavity)
0002417 (abdominal segment of trunk)
0002530 (gland)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003064 (intermediate mesoderm)
0003081 (lateral plate mesoderm)
0003101 (male organism)
0003103 (compound organ)
0003133 (reproductive organ)
0003135 (male reproductive organ)
0003886 (body cavity precursor)
0003887 (intraembryonic coelom)
0003937 (sex gland)
0004054 (internal male genitalia)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004175 (internal genitalia)
0004176 (external genitalia)
0004458 (body cavity or lining)
0004875 (nephrogenic cord)
0004876 (urogenital ridge)
0005095 (kidney rudiment)
0005156 (reproductive structure)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005399 (male reproductive gland)
0005423 (developing anatomical structure)
0005564 (gonad primordium)
0005721 (pronephric mesoderm)
0005754 (rostral part of nephrogenic cord)
0005904 (duct of male reproductive system)
0006554 (urinary system structure)
0006868 (seminal fluid secreting gland)
0006947 (male genital duct)
0007023 (adult organism)
0007687 (kidney field)
0009117 (indifferent gonad)
0009196 (indifferent external genitalia)

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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