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FF:11394-118C8: 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 17:06, 29 March 2012


Name:Fibroblast - Gingival, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuegum
dev stagefetus
sexunknown
agefetal
cell typefibroblast
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number427
catalog numberSC2625
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-0.107
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-0.0991
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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: CNhs12006

Jaspar motifP-value
MA0002.20.174
MA0003.10.26
MA0004.10.919
MA0006.10.609
MA0007.10.26
MA0009.10.372
MA0014.10.199
MA0017.10.211
MA0018.20.0552
MA0019.10.894
MA0024.10.0157
MA0025.10.143
MA0027.10.237
MA0028.10.267
MA0029.10.217
MA0030.10.0467
MA0031.10.122
MA0035.20.131
MA0038.10.535
MA0039.20.179
MA0040.10.144
MA0041.10.0856
MA0042.10.112
MA0043.10.284
MA0046.10.58
MA0047.20.113
MA0048.10.444
MA0050.10.744
MA0051.10.539
MA0052.10.561
MA0055.10.937
MA0057.10.707
MA0058.10.757
MA0059.10.0332
MA0060.10.611
MA0061.19.10635e-4
MA0062.21.69646e-4
MA0065.20.0159
MA0066.10.271
MA0067.10.468
MA0068.10.58
MA0069.10.429
MA0070.10.422
MA0071.10.624
MA0072.10.857
MA0073.10.759
MA0074.10.556
MA0076.10.0655
MA0077.10.517
MA0078.10.727
MA0079.20.12
MA0080.21.11094e-8
MA0081.10.156
MA0083.10.643
MA0084.10.132
MA0087.10.345
MA0088.10.732
MA0090.10.289
MA0091.10.481
MA0092.10.451
MA0093.10.9
MA0099.20.32
MA0100.10.817
MA0101.10.00341
MA0102.20.496
MA0103.15.09818e-4
MA0104.20.1
MA0105.11.35424e-7
MA0106.10.658
MA0107.10.00158
MA0108.20.0653
MA0111.10.0561
MA0112.20.0826
MA0113.10.17
MA0114.10.129
MA0115.10.0902
MA0116.13.19583e-5
MA0117.10.207
MA0119.10.936
MA0122.10.69
MA0124.10.314
MA0125.10.374
MA0131.10.797
MA0135.10.106
MA0136.11.25995e-10
MA0137.20.0367
MA0138.20.807
MA0139.10.398
MA0140.10.146
MA0141.10.663
MA0142.10.109
MA0143.10.461
MA0144.10.414
MA0145.10.946
MA0146.10.26
MA0147.10.0495
MA0148.10.185
MA0149.10.262
MA0150.10.971
MA0152.10.624
MA0153.10.821
MA0154.10.0231
MA0155.10.913
MA0156.11.03917e-6
MA0157.10.761
MA0159.10.0203
MA0160.10.627
MA0162.10.466
MA0163.12.74794e-4
MA0164.10.823
MA0258.10.108
MA0259.10.558



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: CNhs12006

Novel motifP-value
10.0486
100.144
1000.428
1010.764
1020.429
1030.17
1040.897
1050.657
1060.24
1070.669
1080.835
1090.385
110.313
1100.429
1110.121
1120.277
1134.82481e-4
1140.166
1150.8
1160.911
1170.389
1180.33
1190.0217
120.737
1200.734
1210.88
1220.201
1239.55217e-4
1240.159
1250.118
1260.808
1270.568
1280.828
1290.135
130.0189
1300.0647
1310.303
1320.897
1330.759
1340.309
1350.0316
1360.197
1370.0536
1380.257
1390.0069
140.328
1400.255
1410.00821
1420.601
1430.046
1440.473
1450.482
1460.799
1470.279
1480.412
1490.691
150.047
1500.737
1510.478
1520.256
1530.277
1540.484
1550.067
1560.452
1570.55
1580.00201
1590.243
160.81
1600.293
1610.491
1620.462
1630.5
1640.768
1650.354
1660.89
1670.0631
1680.637
1690.875
170.501
180.939
190.417
20.563
200.824
210.68
220.414
230.945
240.638
250.0888
260.214
270.828
280.292
290.512
30.303
300.259
310.925
320.0267
330.812
340.973
350.119
360.00328
370.931
380.349
390.954
40.116
400.0485
410.0585
420.292
430.296
440.0577
450.946
460.202
470.0183
480.163
490.119
50.234
500.354
510.618
520.751
530.353
540.933
550.659
560.591
570.365
580.0502
590.739
60.505
600.252
610.313
620.0499
630.773
640.308
650.61
660.966
670.374
680.592
690.884
70.0676
700.179
710.042
720.787
730.577
740.836
750.0655
760.861
770.77
780.0531
790.404
80.354
800.228
810.384
820.077
830.0252
840.959
850.753
860.842
870.101
880.669
890.38
90.753
900.0126
910.566
920.601
930.276
940.507
950.687
960.17
970.607
980.202
990.0126



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: CNhs12006


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002552 (fibroblast of gingiva)

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000153 (anterior region of body)
0000161 (orifice)
0000165 (mouth)
0000166 (oral opening)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000930 (stomodeum)
0001004 (respiratory system)
0001007 (digestive system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0001828 (gingiva)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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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