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FF:10013-101C4: 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 16:26, 29 March 2012


Name:cervix, 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
tissuecervix
dev stage40,46,57,65 years old adult
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0910061 -4
catalog numberCat:AM6000 Lot:0910061 -4
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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-0.103
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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-Whole0.0322
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: CNhs10618

Jaspar motifP-value
MA0002.20.00264
MA0003.10.381
MA0004.10.0267
MA0006.10.486
MA0007.10.446
MA0009.10.61
MA0014.10.371
MA0017.10.0518
MA0018.20.0824
MA0019.10.42
MA0024.10.194
MA0025.10.625
MA0027.10.595
MA0028.11.01315e-4
MA0029.10.138
MA0030.10.0066
MA0031.10.0527
MA0035.20.0728
MA0038.10.874
MA0039.20.937
MA0040.10.698
MA0041.10.858
MA0042.10.675
MA0043.10.0637
MA0046.10.316
MA0047.20.382
MA0048.10.205
MA0050.10.997
MA0051.10.585
MA0052.10.0168
MA0055.10.00122
MA0057.10.949
MA0058.10.00854
MA0059.16.82312e-4
MA0060.10.0105
MA0061.10.00121
MA0062.21.85327e-7
MA0065.20.0054
MA0066.10.127
MA0067.10.0565
MA0068.17.83677e-5
MA0069.10.861
MA0070.10.242
MA0071.10.073
MA0072.10.157
MA0073.10.63
MA0074.10.989
MA0076.15.48922e-5
MA0077.10.778
MA0078.10.168
MA0079.20.321
MA0080.20.00272
MA0081.10.0659
MA0083.14.64471e-4
MA0084.10.91
MA0087.10.158
MA0088.10.023
MA0090.10.12
MA0091.10.656
MA0092.10.99
MA0093.10.0292
MA0099.24.178e-11
MA0100.10.0873
MA0101.10.00249
MA0102.20.829
MA0103.10.399
MA0104.24.84691e-4
MA0105.12.34383e-6
MA0106.10.112
MA0107.10.00627
MA0108.23.85172e-13
MA0111.10.559
MA0112.20.155
MA0113.10.539
MA0114.10.00886
MA0115.10.0119
MA0116.14.63139e-4
MA0117.10.341
MA0119.10.312
MA0122.10.597
MA0124.10.84
MA0125.10.285
MA0131.10.295
MA0135.10.414
MA0136.11.81828e-4
MA0137.20.855
MA0138.20.615
MA0139.10.226
MA0140.10.0119
MA0141.10.00445
MA0142.10.143
MA0143.10.865
MA0144.10.988
MA0145.10.276
MA0146.10.402
MA0147.12.2197e-4
MA0148.10.83
MA0149.10.0142
MA0150.17.45314e-6
MA0152.10.225
MA0153.10.0619
MA0154.10.0535
MA0155.10.692
MA0156.11.41917e-4
MA0157.10.672
MA0159.10.0606
MA0160.10.0101
MA0162.10.712
MA0163.19.09154e-9
MA0164.10.218
MA0258.10.19
MA0259.10.0431



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: CNhs10618

Novel motifP-value
10.0123
100.0322
1000.0886
1010.916
1020.382
1030.108
1040.595
1050.804
1060.633
1070.36
1080.979
1090.0121
110.0494
1100.171
1110.00282
1120.944
1130.143
1140.00295
1150.436
1160.74
1170.0189
1180.0495
1190.291
120.482
1200.0828
1210.733
1220.89
1230.0611
1240.766
1250.178
1260.768
1270.226
1280.949
1290.349
130.0532
1300.664
1310.289
1320.0685
1330.0049
1340.11
1350.352
1360.347
1370.336
1380.558
1390.311
140.823
1400.212
1410.765
1420.678
1430.00809
1440.781
1450.56
1460.92
1470.751
1480.191
1490.302
150.0335
1500.383
1510.652
1520.705
1530.338
1540.885
1550.351
1560.949
1570.494
1580.435
1590.423
160.233
1600.69
1610.425
1620.167
1630.415
1640.0536
1650.875
1660.242
1670.0268
1680.603
1690.489
170.461
180.0245
190.6
20.149
200.137
210.335
220.977
230.74
240.481
250.304
260.0245
270.98
280.704
290.00863
30.199
300.0439
310.966
320.63
330.138
340.461
350.246
360.0134
370.136
380.486
390.373
40.216
400.0297
410.0452
420.296
430.182
440.354
450.236
460.0935
470.0598
480.181
490.0897
50.511
500.629
510.685
520.356
530.817
540.919
550.932
560.681
570.139
580.565
590.906
60.72
600.86
610.373
620.308
630.521
640.2
650.566
660.0282
670.525
680.75
690.421
70.216
700.0343
710.0366
720.729
730.0593
740.229
750.00913
760.0371
770.41
780.128
790.824
80.178
800.193
810.541
820.854
830.526
840.899
850.765
860.647
870.0412
880.8
890.846
90.596
900.0772
910.712
920.991
930.057
940.0454
950.00543
960.193
970.781
980.102
990.268



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: CNhs10618


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
0000002 (uterine cervix)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
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)
0001560 (neck of organ)
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)
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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