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FF:11667-122G2: 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 17:12, 29 March 2012


Name:Fibroblast - Lymphatic, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelymph node
dev stageNA
sexNA
ageNA
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 numberNA
catalog numberSC2535
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-0.0787
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-0.371
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs12118

Jaspar motifP-value
MA0002.20.0549
MA0003.10.163
MA0004.10.804
MA0006.10.293
MA0007.10.0152
MA0009.10.495
MA0014.10.744
MA0017.10.125
MA0018.20.00362
MA0019.10.693
MA0024.13.12099e-4
MA0025.10.694
MA0027.10.543
MA0028.10.0242
MA0029.10.379
MA0030.10.218
MA0031.10.0401
MA0035.20.0651
MA0038.10.702
MA0039.20.623
MA0040.10.313
MA0041.10.364
MA0042.10.959
MA0043.10.00916
MA0046.10.0698
MA0047.20.866
MA0048.10.809
MA0050.10.246
MA0051.10.555
MA0052.10.141
MA0055.10.502
MA0057.10.155
MA0058.10.846
MA0059.10.582
MA0060.10.0546
MA0061.10.247
MA0062.25.01232e-5
MA0065.20.0337
MA0066.10.249
MA0067.10.0421
MA0068.10.48
MA0069.10.29
MA0070.10.0338
MA0071.10.0386
MA0072.10.788
MA0073.10.969
MA0074.10.0904
MA0076.18.73302e-4
MA0077.10.371
MA0078.10.359
MA0079.20.684
MA0080.20.00474
MA0081.10.0397
MA0083.11.85286e-4
MA0084.10.683
MA0087.10.966
MA0088.10.514
MA0090.10.0268
MA0091.10.00879
MA0092.10.266
MA0093.10.902
MA0099.21.89314e-4
MA0100.10.0943
MA0101.10.527
MA0102.20.0626
MA0103.10.617
MA0104.20.725
MA0105.10.252
MA0106.10.0774
MA0107.10.35
MA0108.20.00719
MA0111.10.708
MA0112.20.00171
MA0113.10.0244
MA0114.10.155
MA0115.10.643
MA0116.10.1
MA0117.10.304
MA0119.10.159
MA0122.10.593
MA0124.10.42
MA0125.10.481
MA0131.10.236
MA0135.10.0249
MA0136.12.32675e-5
MA0137.20.215
MA0138.20.223
MA0139.10.687
MA0140.10.326
MA0141.10.0206
MA0142.10.295
MA0143.10.846
MA0144.10.726
MA0145.10.15
MA0146.10.0231
MA0147.10.896
MA0148.10.61
MA0149.10.752
MA0150.10.284
MA0152.10.343
MA0153.10.117
MA0154.10.0693
MA0155.10.051
MA0156.15.71402e-4
MA0157.10.121
MA0159.10.474
MA0160.10.0625
MA0162.10.104
MA0163.10.0379
MA0164.10.446
MA0258.10.00999
MA0259.10.497



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: CNhs12118

Novel motifP-value
10.56
100.848
1000.821
1010.533
1020.844
1030.262
1040.211
1050.326
1060.0237
1070.0346
1080.296
1090.0495
110.0424
1100.239
1110.792
1120.378
1130.327
1140.346
1150.0484
1160.059
1170.51
1180.808
1190.314
120.44
1200.716
1210.927
1220.881
1230.316
1240.956
1250.371
1260.747
1270.132
1280.0864
1290.102
130.833
1300.186
1310.573
1320.315
1330.942
1340.118
1350.262
1360.659
1370.218
1380.567
1390.115
140.814
1400.29
1410.385
1420.487
1430.00912
1440.97
1450.2
1460.292
1470.201
1480.619
1490.0113
150.62
1500.24
1510.245
1520.0407
1530.559
1540.595
1550.647
1560.764
1570.0975
1580.176
1590.793
160.0882
1600.0451
1610.379
1620.111
1630.455
1640.497
1650.152
1660.414
1670.124
1680.623
1690.0266
170.106
180.0246
190.0757
20.183
200.407
210.207
220.0924
230.172
240.655
250.476
260.0864
270.138
280.251
290.608
30.39
300.218
310.325
321.44809e-8
330.438
340.161
350.842
360.882
370.166
380.409
390.258
40.604
400.0755
410.651
420.74
430.157
440.478
450.312
460.162
470.422
480.258
490.221
50.852
500.296
510.308
520.371
530.986
540.472
550.465
560.304
570.329
580.943
590.0178
60.698
600.162
610.621
620.842
630.185
640.15
650.0423
660.959
670.906
680.0164
690.279
70.993
700.0205
710.233
720.989
730.038
740.721
750.559
760.566
770.0171
780.979
790.0295
80.0636
800.736
810.496
820.183
830.649
840.761
850.0344
860.768
870.143
880.345
890.132
90.143
900.0668
910.281
920.204
930.989
940.323
950.152
960.354
970.516
980.526
990.0183



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: CNhs12118


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)
0002554 (fibroblast of lymphatic vessel)

UBERON: Anatomy
0000055 (vessel)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0001009 (circulatory system)
0001062 (anatomical entity)
0001473 (lymphatic vessel)
0002049 (vasculature)
0002193 (hemolymphoid system)
0002384 (connective tissue)
0002405 (immune system)
0002465 (lymphoid system)
0004111 (anatomical conduit)
0004535 (cardiovascular system)
0004536 (lymph vasculature)
0006558 (lymphatic part of lymphoid system)
0007798 (vascular system)

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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