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FF:10204-103F6: 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:vagina, 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
sex68
ageF
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberR1234283-10
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-penis-0.0104
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-0.41
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs12854

Jaspar motifP-value
MA0002.20.00903
MA0003.10.702
MA0004.10.365
MA0006.10.557
MA0007.10.689
MA0009.10.119
MA0014.10.36
MA0017.10.153
MA0018.20.834
MA0019.10.122
MA0024.10.0411
MA0025.10.573
MA0027.10.817
MA0028.16.80957e-4
MA0029.10.539
MA0030.19.79043e-7
MA0031.10.00136
MA0035.20.202
MA0038.10.611
MA0039.20.743
MA0040.10.0951
MA0041.10.0581
MA0042.10.124
MA0043.10.713
MA0046.10.0133
MA0047.20.0141
MA0048.10.246
MA0050.10.82
MA0051.10.79
MA0052.10.015
MA0055.10.0719
MA0057.10.927
MA0058.10.259
MA0059.10.00676
MA0060.10.255
MA0061.10.0221
MA0062.21.129e-5
MA0065.20.00858
MA0066.10.00906
MA0067.10.501
MA0068.17.33932e-6
MA0069.10.891
MA0070.10.655
MA0071.10.0799
MA0072.10.545
MA0073.10.87
MA0074.10.482
MA0076.17.08353e-5
MA0077.10.558
MA0078.10.381
MA0079.20.28
MA0080.20.602
MA0081.10.423
MA0083.10.00218
MA0084.10.883
MA0087.10.17
MA0088.10.0863
MA0090.10.0218
MA0091.10.882
MA0092.10.773
MA0093.10.367
MA0099.24.95215e-4
MA0100.10.093
MA0101.10.239
MA0102.20.0114
MA0103.10.136
MA0104.20.0116
MA0105.12.8229e-6
MA0106.10.105
MA0107.10.315
MA0108.23.08198e-11
MA0111.10.512
MA0112.20.00588
MA0113.10.137
MA0114.10.0523
MA0115.10.0374
MA0116.13.19712e-5
MA0117.10.478
MA0119.10.687
MA0122.10.6
MA0124.10.489
MA0125.10.387
MA0131.10.464
MA0135.10.0194
MA0136.10.0284
MA0137.23.76052e-6
MA0138.20.542
MA0139.10.151
MA0140.10.518
MA0141.10.01
MA0142.10.0696
MA0143.10.546
MA0144.10.0263
MA0145.10.338
MA0146.10.22
MA0147.10.0025
MA0148.10.0183
MA0149.10.0432
MA0150.10.156
MA0152.10.473
MA0153.10.0488
MA0154.10.0791
MA0155.10.907
MA0156.10.0141
MA0157.10.177
MA0159.10.144
MA0160.10.112
MA0162.10.446
MA0163.13.26858e-11
MA0164.10.587
MA0258.10.0152
MA0259.10.122



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: CNhs12854

Novel motifP-value
10.0158
100.0517
1000.116
1010.366
1020.303
1030.0917
1040.416
1050.806
1060.453
1070.735
1080.991
1090.0156
110.0179
1100.176
1110.00727
1120.384
1130.5
1140.0189
1150.523
1160.313
1170.0165
1180.111
1190.639
120.818
1200.246
1210.659
1220.616
1230.0533
1240.723
1250.021
1260.827
1270.641
1280.677
1290.326
130.0467
1300.433
1310.182
1320.401
1330.534
1340.51
1350.758
1360.527
1370.522
1380.551
1390.382
140.781
1400.413
1410.237
1420.584
1430.0497
1440.689
1450.337
1460.542
1470.568
1480.0495
1490.469
150.0429
1500.491
1510.72
1520.696
1530.959
1540.534
1550.366
1560.485
1570.677
1580.609
1590.499
160.0502
1600.394
1610.202
1620.382
1630.735
1640.0359
1650.732
1660.913
1670.0284
1680.878
1690.0979
170.498
180.109
190.963
20.432
200.285
210.279
220.967
230.395
240.832
250.316
260.0123
270.664
280.776
290.00469
30.11
300.105
310.737
320.0544
330.142
340.373
350.152
360.0189
370.0919
380.649
390.496
40.235
400.0659
410.34
420.272
430.225
440.0425
450.385
460.024
470.0242
480.0804
490.0705
50.4
500.758
510.408
520.411
530.745
540.996
550.923
560.805
570.167
580.571
590.841
60.672
600.997
610.129
620.365
630.495
640.0765
650.6
660.1
670.723
680.453
690.183
70.227
700.0544
710.0156
720.736
730.218
740.558
750.0265
760.139
770.787
780.0588
790.13
80.0435
800.884
810.234
820.184
830.901
840.827
850.782
860.751
870.0671
880.884
890.22
90.566
900.0813
910.884
920.928
930.0247
940.0776
950.00478
960.288
970.801
980.0753
990.732



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: CNhs12854


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)
0000077 (mixed endoderm/mesoderm-derived structure)
0000161 (orifice)
0000162 (cloaca)
0000163 (embryonic cloaca)
0000164 (primitive urogenital sinus)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000990 (reproductive system)
0000996 (vagina)
0001007 (digestive system)
0001046 (hindgut)
0001062 (anatomical entity)
0001353 (anal region)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003064 (intermediate mesoderm)
0003100 (female organism)
0003104 (mesenchyme)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0003975 (internal female genitalia)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004122 (genitourinary system)
0004175 (internal genitalia)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0006866 (terminal part of digestive tract)
0007023 (adult organism)
0007026 (primitive gut)
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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