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FF:14302-155B9: 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 17:22, 29 March 2012


Name:Fibroblast - skin normal, donor2 (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
age3 year old child
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-penis0.231
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-lymphoma0.592
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: CNhs12582

Jaspar motifP-value
MA0002.20.00105
MA0003.10.0102
MA0004.10.268
MA0006.10.695
MA0007.10.321
MA0009.10.644
MA0014.10.321
MA0017.18.67843e-4
MA0018.20.712
MA0019.10.0731
MA0024.10.0172
MA0025.10.0454
MA0027.10.583
MA0028.10.384
MA0029.10.673
MA0030.10.0284
MA0031.10.0152
MA0035.22.28334e-4
MA0038.10.469
MA0039.20.348
MA0040.10.404
MA0041.10.258
MA0042.10.356
MA0043.10.103
MA0046.10.177
MA0047.20.105
MA0048.10.00346
MA0050.10.0337
MA0051.10.0189
MA0052.10.686
MA0055.10.143
MA0057.10.588
MA0058.10.109
MA0059.10.0997
MA0060.10.432
MA0061.11.56567e-4
MA0062.20.957
MA0065.26.31487e-5
MA0066.10.253
MA0067.10.996
MA0068.10.712
MA0069.10.0313
MA0070.10.347
MA0071.10.0609
MA0072.10.067
MA0073.10.898
MA0074.10.187
MA0076.10.15
MA0077.10.781
MA0078.10.341
MA0079.20.228
MA0080.22.33642e-9
MA0081.10.158
MA0083.10.0107
MA0084.10.195
MA0087.10.582
MA0088.10.964
MA0090.10.0334
MA0091.10.105
MA0092.10.694
MA0093.10.312
MA0099.20.363
MA0100.10.222
MA0101.10.00124
MA0102.20.242
MA0103.18.20781e-6
MA0104.20.0181
MA0105.11.29794e-5
MA0106.10.791
MA0107.13.06238e-4
MA0108.20.0915
MA0111.10.227
MA0112.20.00434
MA0113.10.588
MA0114.10.00122
MA0115.10.205
MA0116.10.125
MA0117.10.927
MA0119.10.51
MA0122.10.761
MA0124.10.589
MA0125.10.942
MA0131.10.181
MA0135.10.195
MA0136.18.60564e-8
MA0137.20.161
MA0138.20.179
MA0139.10.0593
MA0140.10.0358
MA0141.10.00292
MA0142.10.212
MA0143.10.521
MA0144.10.141
MA0145.10.465
MA0146.10.0481
MA0147.10.101
MA0148.10.0113
MA0149.10.785
MA0150.10.0905
MA0152.10.0538
MA0153.10.574
MA0154.10.00112
MA0155.10.0866
MA0156.10.0198
MA0157.10.0192
MA0159.10.0435
MA0160.10.00115
MA0162.10.765
MA0163.10.24
MA0164.10.423
MA0258.10.0117
MA0259.10.392



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: CNhs12582

Novel motifP-value
10.194
100.699
1000.823
1010.865
1020.567
1030.0114
1040.747
1050.34
1060.033
1070.698
1080.877
1090.0375
110.102
1100.552
1110.199
1120.165
1130.386
1140.064
1150.989
1160.943
1170.316
1180.33
1190.0927
120.758
1200.0525
1210.615
1220.117
1230.872
1240.0874
1250.811
1260.073
1270.129
1280.0404
1290.0604
130.761
1300.816
1310.194
1320.57
1330.711
1340.825
1350.898
1360.235
1370.692
1380.255
1390.00944
140.61
1400.147
1410.0765
1420.244
1430.0149
1440.965
1450.841
1460.415
1470.459
1480.162
1490.784
150.0361
1500.991
1510.297
1520.586
1530.631
1540.255
1550.128
1560.411
1570.109
1580.341
1590.317
160.382
1600.0396
1610.129
1620.424
1630.611
1640.977
1650.59
1660.147
1670.884
1680.48
1690.0564
170.459
180.291
190.756
20.415
200.992
210.315
220.208
230.183
240.125
250.17
260.927
270.146
280.852
290.461
30.636
300.71
310.382
320.0076
330.302
340.619
350.123
360.189
370.313
380.289
390.95
40.469
400.0641
410.0378
420.526
430.245
440.0376
450.317
460.289
470.253
480.528
490.185
50.398
500.708
510.272
520.406
530.941
540.399
550.585
560.342
570.879
580.0629
590.0188
60.455
600.0907
610.219
620.0349
630.55
640.134
650.17
660.892
670.866
680.581
690.776
70.158
700.00389
710.369
720.204
730.384
740.407
750.133
760.991
770.311
780.124
790.283
80.133
800.281
810.422
820.0876
830.2
840.865
850.063
860.815
870.754
880.62
890.104
90.559
900.258
910.824
920.396
930.459
940.226
950.193
960.588
970.748
980.11
990.825



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: CNhs12582


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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