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FF:11450-119A1: 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 17:09, 29 March 2012


Name:Fibroblast - Dermal, donor4
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
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 number243
catalog numberSC2305
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-0.167
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-lymphoma0.569
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12052

Jaspar motifP-value
MA0002.20.0253
MA0003.10.353
MA0004.10.973
MA0006.10.752
MA0007.10.51
MA0009.10.106
MA0014.10.979
MA0017.10.127
MA0018.20.537
MA0019.10.44
MA0024.11.26329e-8
MA0025.10.505
MA0027.10.68
MA0028.13.37062e-4
MA0029.10.829
MA0030.10.00289
MA0031.10.00871
MA0035.20.0387
MA0038.14.84918e-4
MA0039.20.669
MA0040.10.682
MA0041.10.318
MA0042.10.341
MA0043.10.303
MA0046.10.361
MA0047.20.451
MA0048.19.39688e-4
MA0050.19.58613e-7
MA0051.11.69048e-5
MA0052.10.783
MA0055.16.71979e-4
MA0057.10.662
MA0058.10.732
MA0059.10.634
MA0060.12.20524e-13
MA0061.10.00209
MA0062.20.0386
MA0065.20.0677
MA0066.10.227
MA0067.10.145
MA0068.10.792
MA0069.10.794
MA0070.10.112
MA0071.10.85
MA0072.10.951
MA0073.10.593
MA0074.10.661
MA0076.14.29574e-4
MA0077.10.809
MA0078.10.93
MA0079.20.469
MA0080.28.04581e-11
MA0081.10.199
MA0083.10.414
MA0084.10.164
MA0087.10.56
MA0088.10.00124
MA0090.10.844
MA0091.10.404
MA0092.10.194
MA0093.10.937
MA0099.20.579
MA0100.10.0423
MA0101.10.119
MA0102.20.00715
MA0103.12.40151e-4
MA0104.20.0818
MA0105.10.0081
MA0106.10.204
MA0107.10.00843
MA0108.20.325
MA0111.10.563
MA0112.23.8312e-4
MA0113.10.938
MA0114.10.393
MA0115.10.833
MA0116.10.119
MA0117.10.804
MA0119.10.816
MA0122.10.278
MA0124.10.757
MA0125.10.414
MA0131.10.132
MA0135.10.495
MA0136.12.61183e-6
MA0137.20.121
MA0138.20.529
MA0139.10.545
MA0140.10.236
MA0141.10.938
MA0142.10.121
MA0143.10.41
MA0144.10.0568
MA0145.10.0488
MA0146.10.375
MA0147.10.145
MA0148.10.288
MA0149.10.995
MA0150.10.0945
MA0152.10.0407
MA0153.10.461
MA0154.10.00471
MA0155.10.133
MA0156.10.142
MA0157.10.0111
MA0159.10.0107
MA0160.10.181
MA0162.10.524
MA0163.10.646
MA0164.10.937
MA0258.10.00131
MA0259.10.238



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: CNhs12052

Novel motifP-value
10.366
100.348
1000.927
1010.387
1020.54
1030.217
1040.799
1050.979
1068.33331e-5
1070.0944
1080.183
1090.751
110.823
1100.687
1110.971
1120.0319
1130.00552
1140.195
1150.728
1160.695
1170.88
1180.909
1190.118
120.797
1200.201
1210.628
1220.23
1230.0414
1240.253
1250.819
1260.78
1270.297
1280.0117
1290.113
130.943
1300.0163
1310.313
1320.883
1330.679
1340.605
1350.0329
1360.239
1370.123
1380.102
1391.10283e-5
140.194
1400.978
1410.808
1420.674
1430.37
1440.534
1450.982
1460.715
1470.964
1480.236
1490.233
150.167
1500.911
1510.138
1520.0594
1530.218
1540.546
1550.0292
1560.548
1570.103
1580.029
1590.0444
160.77
1600.96
1610.562
1620.448
1630.653
1640.681
1650.466
1660.854
1670.337
1680.457
1690.0628
170.19
180.799
190.554
20.574
200.353
210.279
220.377
230.0209
240.857
250.736
260.973
270.514
280.555
290.795
30.539
300.758
310.647
320.839
330.444
340.306
350.502
360.339
370.396
380.262
390.794
40.232
400.211
410.129
420.741
430.236
440.806
450.0803
460.281
470.916
480.843
490.181
50.0968
500.779
510.481
520.0812
530.156
540.439
550.421
560.678
570.614
580.149
590.306
60.661
600.022
610.948
620.122
630.552
640.653
650.119
660.0387
670.75
680.995
690.883
70.336
700.00439
710.62
720.211
730.448
740.242
750.413
760.837
770.541
780.428
790.546
80.646
800.105
810.394
820.0187
830.306
840.934
850.00673
860.542
870.0993
880.492
890.0921
90.63
900.666
910.348
920.0887
930.895
940.336
950.429
960.288
970.672
980.184
990.0626



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: CNhs12052


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)
0002551 (fibroblast of dermis)
0002620 (skin fibroblast)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002067 (dermis)
0002097 (skin of body)
0002199 (integument)
0002329 (somite)
0002384 (connective tissue)
0002416 (integumental system)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003102 (surface structure)
0003104 (mesenchyme)
0004016 (dermatome)
0004120 (mesoderm-derived structure)
0004290 (dermomyotome)
0004923 (organ component layer)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
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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