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FF:10055-101H1: 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 16:51, 29 March 2012


Name:uterus, fetal, donor1
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 stage26 weeks fetus
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB402230
catalog numberCat:RtHFN: Uterus
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-0.0774
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: CNhs11763

Jaspar motifP-value
MA0002.21.67785e-5
MA0003.10.212
MA0004.10.0369
MA0006.10.767
MA0007.10.539
MA0009.10.203
MA0014.10.284
MA0017.10.00352
MA0018.20.0957
MA0019.10.909
MA0024.10.349
MA0025.10.0571
MA0027.10.767
MA0028.10.00187
MA0029.10.474
MA0030.10.785
MA0031.10.973
MA0035.20.167
MA0038.10.256
MA0039.20.751
MA0040.10.257
MA0041.10.508
MA0042.10.844
MA0043.10.00741
MA0046.10.849
MA0047.20.0633
MA0048.10.751
MA0050.10.00262
MA0051.10.00244
MA0052.10.477
MA0055.10.0844
MA0057.10.804
MA0058.10.00742
MA0059.10.0027
MA0060.10.307
MA0061.13.09672e-4
MA0062.22.48648e-7
MA0065.23.81654e-4
MA0066.10.0993
MA0067.10.0369
MA0068.18.55126e-6
MA0069.10.404
MA0070.10.347
MA0071.10.15
MA0072.10.294
MA0073.10.327
MA0074.10.887
MA0076.19.56098e-4
MA0077.10.828
MA0078.10.464
MA0079.20.957
MA0080.25.15652e-8
MA0081.10.0123
MA0083.10.0805
MA0084.10.301
MA0087.10.146
MA0088.10.0288
MA0090.10.377
MA0091.10.918
MA0092.10.447
MA0093.10.0387
MA0099.21.29286e-18
MA0100.10.379
MA0101.13.37668e-4
MA0102.20.0499
MA0103.10.394
MA0104.20.00321
MA0105.17.88965e-8
MA0106.10.111
MA0107.16.86814e-4
MA0108.21.25541e-9
MA0111.10.855
MA0112.20.00307
MA0113.10.622
MA0114.10.00149
MA0115.10.00283
MA0116.12.37807e-4
MA0117.10.282
MA0119.10.252
MA0122.10.859
MA0124.10.241
MA0125.10.413
MA0131.10.813
MA0135.10.374
MA0136.14.04735e-11
MA0137.20.573
MA0138.20.603
MA0139.10.0669
MA0140.10.231
MA0141.10.00481
MA0142.10.0809
MA0143.10.514
MA0144.10.706
MA0145.10.868
MA0146.10.101
MA0147.10.00299
MA0148.10.0239
MA0149.10.0129
MA0150.14.9565e-9
MA0152.10.0249
MA0153.10.16
MA0154.10.0013
MA0155.10.951
MA0156.17.86274e-7
MA0157.10.626
MA0159.10.0147
MA0160.10.00132
MA0162.10.564
MA0163.11.02523e-7
MA0164.10.288
MA0258.10.0366
MA0259.10.324



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: CNhs11763

Novel motifP-value
10.01
100.0443
1000.311
1010.53
1020.526
1030.247
1040.712
1050.873
1060.238
1070.678
1080.877
1090.00727
110.0801
1100.191
1110.0086
1120.211
1130.0367
1147.1111e-4
1150.184
1160.933
1170.00414
1180.0792
1190.409
120.278
1200.388
1210.751
1220.306
1230.0552
1240.895
1250.278
1260.519
1270.0687
1280.543
1290.775
130.0657
1300.36
1310.91
1320.129
1330.972
1340.843
1350.777
1360.652
1370.134
1380.252
1390.155
140.403
1400.865
1410.602
1420.592
1430.0209
1440.777
1450.839
1460.412
1470.821
1480.0233
1490.659
150.0275
1500.486
1510.357
1520.222
1530.846
1540.913
1550.0806
1560.61
1570.522
1580.12
1590.621
160.412
1600.704
1610.624
1620.135
1630.534
1640.0444
1650.441
1660.0886
1670.0261
1680.242
1690.0252
170.325
180.0299
191
20.602
200.231
210.399
220.465
230.666
240.108
250.31
260.0212
270.733
280.668
290.0208
30.213
300.135
310.843
320.0128
330.188
340.652
350.166
360.0205
370.0206
380.27
390.668
40.9
400.0635
410.0256
420.23
430.13
440.958
450.527
460.136
470.0539
480.227
490.108
50.27
500.936
510.565
520.712
530.815
540.668
550.602
560.511
570.198
580.408
590.354
60.963
600.402
610.352
620.218
630.398
640.36
650.324
660.757
670.468
680.448
690.606
70.153
700.0179
710.0477
720.313
730.0195
740.477
750.00437
760.136
770.813
780.172
790.822
80.09
800.581
810.676
820.373
830.596
840.725
850.327
860.0759
870.0188
880.801
890.312
90.826
900.177
910.502
920.433
930.202
940.0341
950.00602
960.0999
970.932
980.131
990.416



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: CNhs11763


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)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000479 (tissue)
0000922 (embryo)
0001062 (anatomical entity)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0005795 (embryonic uterus)

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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