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FF:10100-102D1: 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 16:48, 29 March 2012


Name:uterus, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueuterus
dev stage23-63 years old adult
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number8101369A-20
catalog numberCat: 636643 Lot: 8101369A-20
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
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-0.121
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
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: CNhs11676

Jaspar motifP-value
MA0002.20.00685
MA0003.10.815
MA0004.10.2
MA0006.10.984
MA0007.10.197
MA0009.10.15
MA0014.10.221
MA0017.10.0204
MA0018.20.957
MA0019.10.461
MA0024.10.322
MA0025.10.914
MA0027.10.651
MA0028.10.0298
MA0029.10.516
MA0030.11.24182e-4
MA0031.10.0146
MA0035.20.496
MA0038.10.564
MA0039.20.856
MA0040.10.704
MA0041.10.443
MA0042.10.194
MA0043.10.484
MA0046.10.00941
MA0047.20.243
MA0048.10.397
MA0050.10.73
MA0051.10.768
MA0052.11.29844e-4
MA0055.10.0308
MA0057.10.874
MA0058.10.124
MA0059.10.00397
MA0060.10.159
MA0061.10.0114
MA0062.20.00289
MA0065.28.37697e-4
MA0066.10.00762
MA0067.10.248
MA0068.13.07624e-4
MA0069.10.803
MA0070.10.476
MA0071.10.087
MA0072.10.302
MA0073.10.461
MA0074.10.569
MA0076.10.115
MA0077.10.918
MA0078.10.163
MA0079.20.435
MA0080.20.0534
MA0081.10.326
MA0083.11.11603e-5
MA0084.10.984
MA0087.10.217
MA0088.10.098
MA0090.10.211
MA0091.10.435
MA0092.10.494
MA0093.10.222
MA0099.23.06285e-9
MA0100.10.227
MA0101.10.0474
MA0102.20.522
MA0103.10.059
MA0104.20.0136
MA0105.15.54399e-7
MA0106.10.0753
MA0107.10.0832
MA0108.21.61126e-11
MA0111.10.5
MA0112.20.00479
MA0113.10.842
MA0114.10.00884
MA0115.10.012
MA0116.12.51763e-4
MA0117.10.404
MA0119.10.213
MA0122.10.297
MA0124.10.357
MA0125.10.241
MA0131.10.782
MA0135.10.24
MA0136.10.0213
MA0137.20.306
MA0138.20.926
MA0139.10.269
MA0140.10.0977
MA0141.10.00771
MA0142.10.085
MA0143.10.93
MA0144.10.925
MA0145.10.844
MA0146.10.172
MA0147.10.00719
MA0148.10.495
MA0149.10.0284
MA0150.12.10536e-4
MA0152.10.243
MA0153.17.50493e-4
MA0154.10.0146
MA0155.10.904
MA0156.10.0694
MA0157.10.359
MA0159.10.0413
MA0160.10.0166
MA0162.10.185
MA0163.12.38296e-9
MA0164.10.216
MA0258.10.0236
MA0259.10.149



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: CNhs11676

Novel motifP-value
10.0091
100.0369
1000.101
1010.743
1020.252
1030.0287
1040.483
1050.448
1060.1
1070.72
1080.327
1090.0149
110.0316
1100.147
1116.51673e-4
1120.472
1130.286
1140.00648
1150.472
1160.399
1170.0149
1180.0764
1190.167
120.873
1200.0618
1210.718
1220.93
1230.106
1240.849
1250.0894
1260.683
1270.0832
1280.335
1290.516
130.0784
1300.501
1310.262
1320.221
1330.0275
1340.256
1350.32
1360.376
1370.208
1380.452
1390.211
140.982
1400.192
1410.596
1420.453
1430.0155
1440.918
1450.397
1460.884
1470.919
1480.00669
1490.635
150.0434
1500.203
1510.38
1520.324
1530.402
1540.741
1550.159
1560.69
1570.584
1580.785
1590.295
160.0584
1600.361
1610.398
1620.348
1630.368
1640.0894
1650.704
1660.15
1670.0113
1680.605
1690.0449
170.245
180.0258
190.941
20.408
200.245
210.206
220.65
230.976
240.431
250.316
260.00177
270.708
280.703
290.0161
30.149
300.116
310.649
320.38
330.138
340.466
350.206
360.00788
370.083
380.527
390.546
40.521
400.0318
410.107
420.361
430.135
440.125
450.543
460.0527
470.0381
480.133
490.0702
50.494
500.887
510.522
520.768
530.945
540.751
550.672
560.602
570.154
580.523
590.453
60.742
600.553
610.371
620.269
630.209
640.166
650.457
660.13
670.326
680.963
690.125
70.222
700.0152
710.0236
720.371
730.0564
740.531
750.00817
760.0991
770.976
780.075
790.346
80.0567
800.321
810.175
820.604
830.918
840.631
850.287
860.442
870.00504
880.961
890.394
90.789
900.0538
910.872
920.723
930.238
940.0106
950.00404
960.281
970.665
980.181
990.814



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: CNhs11676


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)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000995 (uterus)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003100 (female organism)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0003975 (internal female genitalia)
0004120 (mesoderm-derived structure)
0004175 (internal genitalia)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005795 (embryonic uterus)
0006834 (uterus or analog)
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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