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FF:11345-117G4: 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 16:47, 29 March 2012


Name:Fibroblast - Cardiac, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueheart
dev stage21 weeks old fetus
sexfemale
ageemrbyo 21week
cell typefibroblast
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2112
catalog numberCA306-R10f
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-0.168
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-0.124
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: CNhs11378

Jaspar motifP-value
MA0002.20.189
MA0003.10.188
MA0004.10.455
MA0006.10.278
MA0007.10.0819
MA0009.10.208
MA0014.10.631
MA0017.10.723
MA0018.20.0148
MA0019.10.621
MA0024.10.0357
MA0025.10.776
MA0027.10.703
MA0028.10.205
MA0029.10.202
MA0030.10.162
MA0031.10.0318
MA0035.20.353
MA0038.10.962
MA0039.20.854
MA0040.10.447
MA0041.10.343
MA0042.10.819
MA0043.10.00511
MA0046.10.636
MA0047.20.754
MA0048.10.266
MA0050.13.3178e-9
MA0051.17.86287e-4
MA0052.10.868
MA0055.10.0742
MA0057.10.298
MA0058.10.167
MA0059.10.247
MA0060.10.293
MA0061.10.144
MA0062.20.00629
MA0065.20.0939
MA0066.10.177
MA0067.10.0411
MA0068.10.932
MA0069.10.339
MA0070.10.585
MA0071.10.282
MA0072.10.525
MA0073.10.421
MA0074.10.266
MA0076.10.0244
MA0077.10.041
MA0078.10.142
MA0079.20.883
MA0080.20.00155
MA0081.10.0809
MA0083.14.52996e-8
MA0084.10.365
MA0087.10.598
MA0088.10.3
MA0090.10.00211
MA0091.10.0393
MA0092.10.028
MA0093.10.411
MA0099.22.91631e-7
MA0100.10.132
MA0101.10.184
MA0102.20.0733
MA0103.10.727
MA0104.20.491
MA0105.10.13
MA0106.10.201
MA0107.10.211
MA0108.22.6263e-5
MA0111.10.0763
MA0112.20.00159
MA0113.10.212
MA0114.10.577
MA0115.10.406
MA0116.10.0841
MA0117.10.841
MA0119.10.0525
MA0122.10.492
MA0124.10.98
MA0125.10.992
MA0131.10.383
MA0135.10.577
MA0136.10.0027
MA0137.20.0969
MA0138.20.554
MA0139.10.671
MA0140.10.396
MA0141.10.372
MA0142.10.198
MA0143.10.955
MA0144.10.69
MA0145.10.137
MA0146.10.12
MA0147.10.903
MA0148.10.869
MA0149.10.402
MA0150.10.109
MA0152.10.126
MA0153.10.43
MA0154.10.0406
MA0155.10.0407
MA0156.10.297
MA0157.10.064
MA0159.10.0329
MA0160.10.568
MA0162.10.0593
MA0163.10.0206
MA0164.10.755
MA0258.10.00323
MA0259.10.966



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: CNhs11378

Novel motifP-value
10.217
100.842
1000.587
1010.383
1020.779
1030.408
1040.195
1050.153
1060.0119
1070.0189
1080.463
1090.0829
110.0555
1100.353
1110.817
1120.658
1130.625
1140.261
1150.172
1160.0743
1170.876
1180.743
1190.0743
120.892
1200.203
1210.502
1220.932
1230.0813
1240.972
1250.988
1260.611
1270.468
1280.185
1290.788
130.599
1300.557
1310.194
1320.351
1330.982
1340.794
1350.0482
1360.666
1370.476
1380.546
1390.0511
140.761
1400.872
1410.592
1420.427
1430.00832
1440.83
1450.156
1460.176
1470.411
1480.622
1490.0189
150.336
1500.0639
1510.62
1520.0319
1530.813
1540.799
1550.259
1560.346
1570.759
1580.177
1590.638
160.173
1600.041
1610.403
1620.294
1630.425
1640.522
1650.326
1660.832
1670.498
1680.949
1690.0243
170.105
180.0479
190.0382
20.527
200.427
210.753
220.159
230.00858
240.246
250.579
260.0566
270.604
280.259
290.846
30.44
300.512
310.553
324.97656e-8
330.575
340.137
350.902
360.81
370.118
380.558
390.33
40.25
400.207
410.671
420.609
430.173
440.484
450.346
460.0722
470.24
480.0624
490.206
50.371
500.724
510.654
520.649
530.629
540.355
550.868
560.657
570.234
580.888
590.00809
60.697
600.448
610.903
620.257
630.294
640.129
650.0442
660.444
670.269
680.0711
690.676
70.599
700.199
710.12
720.711
730.0291
740.903
750.485
760.525
770.033
780.428
790.00329
80.0588
800.513
810.79
820.747
830.592
840.672
850.0241
860.799
870.0721
880.112
890.0434
90.337
900.674
910.181
920.79
930.772
940.237
950.249
960.79
970.259
980.876
990.0345



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: CNhs11378


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)
0002494 (cardiocyte)
0002548 (cardiac fibroblast)

UBERON: Anatomy
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000948 (heart)
0001009 (circulatory system)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003084 (heart primordium)
0003914 (epithelial tube)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0007005 (cardiac mesoderm)
0007100 (primary circulatory organ)

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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