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FF:14323-155E3: 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 17:19, 29 March 2012


Name:Fibroblast - skin normal, donor1 (nuclear fraction)
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 stageNA
sexM
age25 year old
cell typefibroblast
cell lineNA
companyCoriell
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-0.109
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-0.0176
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs12403

Jaspar motifP-value
MA0002.20.105
MA0003.10.991
MA0004.10.0217
MA0006.10.465
MA0007.10.537
MA0009.10.22
MA0014.10.182
MA0017.10.0497
MA0018.20.195
MA0019.10.783
MA0024.10.00152
MA0025.10.0974
MA0027.10.815
MA0028.10.413
MA0029.10.722
MA0030.10.159
MA0031.10.17
MA0035.25.23208e-4
MA0038.10.43
MA0039.20.321
MA0040.10.198
MA0041.10.731
MA0042.10.667
MA0043.10.117
MA0046.10.316
MA0047.20.968
MA0048.10.00634
MA0050.10.577
MA0051.10.145
MA0052.10.108
MA0055.10.303
MA0057.10.676
MA0058.10.00281
MA0059.10.0444
MA0060.12.07666e-4
MA0061.10.0118
MA0062.20.506
MA0065.20.00174
MA0066.10.451
MA0067.10.645
MA0068.10.248
MA0069.10.0413
MA0070.10.65
MA0071.10.154
MA0072.10.438
MA0073.10.72
MA0074.10.612
MA0076.10.0984
MA0077.10.0759
MA0078.10.655
MA0079.20.318
MA0080.21.52063e-7
MA0081.10.0289
MA0083.13.29492e-5
MA0084.10.289
MA0087.10.691
MA0088.10.829
MA0090.12.18488e-5
MA0091.10.824
MA0092.10.869
MA0093.10.0243
MA0099.20.319
MA0100.10.597
MA0101.10.00171
MA0102.20.519
MA0103.17.27761e-6
MA0104.29.43344e-5
MA0105.10.0647
MA0106.10.132
MA0107.10.00158
MA0108.20.0885
MA0111.10.0953
MA0112.20.563
MA0113.10.819
MA0114.10.0171
MA0115.10.189
MA0116.10.874
MA0117.10.365
MA0119.10.901
MA0122.10.474
MA0124.10.0517
MA0125.10.153
MA0131.10.993
MA0135.10.875
MA0136.11.05811e-5
MA0137.20.785
MA0138.20.753
MA0139.10.492
MA0140.10.00497
MA0141.10.0297
MA0142.10.0208
MA0143.10.658
MA0144.10.881
MA0145.10.413
MA0146.10.926
MA0147.10.00395
MA0148.10.347
MA0149.10.0953
MA0150.10.18
MA0152.10.0743
MA0153.10.805
MA0154.10.936
MA0155.10.947
MA0156.10.0431
MA0157.10.206
MA0159.10.436
MA0160.10.00573
MA0162.10.096
MA0163.10.533
MA0164.10.496
MA0258.10.503
MA0259.10.336



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: CNhs12403

Novel motifP-value
10.082
100.446
1000.376
1010.778
1020.0295
1030.167
1040.385
1050.731
1060.0379
1070.753
1080.868
1090.0982
110.191
1100.854
1110.0895
1120.667
1130.0153
1140.685
1150.861
1160.88
1170.511
1180.687
1190.546
120.869
1200.498
1210.803
1220.0479
1230.00901
1240.0943
1250.706
1260.179
1270.763
1280.131
1290.328
130.412
1300.664
1310.687
1320.627
1330.616
1340.828
1350.538
1360.177
1370.45
1380.391
1390.351
140.46
1400.923
1410.538
1420.931
1430.316
1440.992
1450.92
1460.187
1470.0783
1480.0606
1490.118
150.0233
1500.617
1510.237
1520.535
1530.615
1540.523
1550.00826
1560.505
1570.99
1580.248
1590.232
160.91
1600.364
1610.353
1620.562
1630.81
1640.459
1650.514
1660.0292
1670.226
1680.893
1690.281
170.799
180.624
190.182
20.7
200.559
210.158
220.895
230.587
240.171
250.109
260.818
270.398
280.672
290.863
30.673
300.502
310.671
323.08185e-7
330.402
340.782
350.637
360.0347
370.64
380.362
390.486
40.231
400.0246
410.453
420.268
430.443
440.157
450.463
460.493
470.134
480.413
490.0529
50.807
500.525
510.448
520.762
530.358
540.557
550.409
560.297
570.448
580.137
590.925
60.612
600.199
610.171
620.144
630.665
640.121
650.651
660.225
670.902
680.562
690.351
70.0955
700.359
710.398
720.36
730.315
740.38
750.353
760.896
770.53
780.0292
790.00724
80.0954
800.836
810.412
820.798
830.0436
840.124
850.433
860.606
870.393
880.645
890.845
90.838
900.159
910.996
920.711
930.642
940.716
950.343
960.944
970.521
980.0593
990.156



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: CNhs12403


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)
0002620 (skin fibroblast)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0001062 (anatomical entity)
0002097 (skin of body)
0002199 (integument)
0002384 (connective tissue)
0002416 (integumental system)
0003102 (surface structure)

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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