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FF:11268-116G8: Difference between revisions

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|creation_date=
|creation_date=
|def="A fibroblast from cardiac tissue." [GOC:tfm]
|def="A fibroblast from cardiac tissue." [GOC:tfm]
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:20, 29 March 2012


Name:Fibroblast - Cardiac, donor1
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 stage22 weeks old fetus
sexmale
ageembryo 22week
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 number1592
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-penis0
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-lymphoma0.0143
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
C113-thyroid-throat-lung-lymph-small-colon-trachea0
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs12498

Jaspar motifP-value
MA0002.20.128
MA0003.10.484
MA0004.10.498
MA0006.10.116
MA0007.10.42
MA0009.10.232
MA0014.10.402
MA0017.10.904
MA0018.25.37713e-5
MA0019.10.262
MA0024.10.0178
MA0025.10.0634
MA0027.10.475
MA0028.10.00897
MA0029.10.0355
MA0030.10.354
MA0031.10.0202
MA0035.20.414
MA0038.10.353
MA0039.20.933
MA0040.10.808
MA0041.10.339
MA0042.10.632
MA0043.13.45333e-5
MA0046.10.278
MA0047.20.297
MA0048.10.626
MA0050.11.07886e-6
MA0051.10.00499
MA0052.10.482
MA0055.10.831
MA0057.10.112
MA0058.10.175
MA0059.10.811
MA0060.10.118
MA0061.10.0361
MA0062.21.26894e-7
MA0065.20.446
MA0066.10.63
MA0067.10.0137
MA0068.10.854
MA0069.10.619
MA0070.10.816
MA0071.10.649
MA0072.10.396
MA0073.10.871
MA0074.10.577
MA0076.12.94022e-4
MA0077.10.837
MA0078.10.266
MA0079.20.348
MA0080.22.00488e-9
MA0081.16.63092e-4
MA0083.13.2595e-5
MA0084.10.777
MA0087.10.922
MA0088.10.593
MA0090.13.63992e-5
MA0091.10.0433
MA0092.10.169
MA0093.10.456
MA0099.20.427
MA0100.10.0454
MA0101.10.0184
MA0102.20.0171
MA0103.10.264
MA0104.20.115
MA0105.10.0839
MA0106.10.161
MA0107.10.0148
MA0108.24.78383e-11
MA0111.10.261
MA0112.20.148
MA0113.10.592
MA0114.10.298
MA0115.10.0302
MA0116.10.702
MA0117.10.325
MA0119.10.167
MA0122.10.973
MA0124.10.0843
MA0125.10.41
MA0131.10.155
MA0135.10.211
MA0136.15.47247e-9
MA0137.20.447
MA0138.20.467
MA0139.10.979
MA0140.10.429
MA0141.10.472
MA0142.10.857
MA0143.10.916
MA0144.10.757
MA0145.10.215
MA0146.10.748
MA0147.10.264
MA0148.10.444
MA0149.10.961
MA0150.10.11
MA0152.10.214
MA0153.10.272
MA0154.10.634
MA0155.10.196
MA0156.15.89231e-7
MA0157.10.0701
MA0159.10.57
MA0160.10.271
MA0162.10.0533
MA0163.10.9
MA0164.10.881
MA0258.10.579
MA0259.10.903



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: CNhs12498

Novel motifP-value
10.586
100.0411
1000.861
1010.077
1020.703
1030.448
1040.642
1050.735
1060.318
1070.0356
1080.224
1090.675
110.595
1100.672
1110.148
1120.681
1130.271
1140.948
1150.0218
1160.0413
1170.12
1180.881
1190.801
120.73
1200.372
1210.951
1220.654
1236.13859e-4
1240.242
1250.317
1260.446
1270.938
1280.271
1290.317
130.771
1300.678
1310.249
1320.385
1330.609
1340.665
1350.474
1360.892
1370.00978
1380.167
1390.542
140.356
1400.989
1410.563
1420.707
1430.552
1440.912
1450.533
1460.341
1470.211
1480.0804
1490.0191
150.735
1500.248
1510.973
1520.0655
1530.643
1540.207
1550.162
1560.35
1570.135
1580.0117
1590.847
160.0711
1600.0316
1610.425
1620.787
1630.989
1640.565
1650.353
1660.158
1670.371
1680.985
1690.0631
170.544
180.55
190.0298
20.158
200.301
210.777
220.275
230.434
240.734
250.317
260.593
270.501
280.0959
290.891
30.652
300.127
310.231
321.33199e-11
330.604
340.379
350.537
360.0576
370.996
380.705
390.251
40.843
400.923
410.8
420.479
430.922
440.229
450.516
460.718
470.906
480.791
490.721
50.75
500.901
510.893
520.402
530.138
540.81
550.829
560.983
570.954
580.157
590.0833
60.599
600.989
610.639
620.442
630.594
640.995
650.471
660.663
670.619
680.716
690.12
70.515
700.721
710.651
720.891
730.0437
740.662
750.579
760.152
770.0123
780.374
790.0105
80.184
800.584
810.799
820.375
830.598
840.586
850.271
860.791
870.109
880.324
890.0547
90.645
900.00869
910.642
920.976
930.511
940.923
950.896
960.706
970.714
980.774
990.00748



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: CNhs12498


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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