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FF:11752-123G6: 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 17:18, 29 March 2012


Name:mesenchymal precursor cell - 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 stageNA
sexNA
ageNA
cell typemesenchymal precursor cell
cell lineNA
companyNA
collaborationClaudio Schneider LNCIB
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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-lymphoma-0.46
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
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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: CNhs12368

Jaspar motifP-value
MA0002.20.835
MA0003.10.353
MA0004.10.105
MA0006.10.7
MA0007.10.758
MA0009.10.446
MA0014.10.419
MA0017.10.357
MA0018.20.0155
MA0019.10.756
MA0024.14.49164e-9
MA0025.10.264
MA0027.10.98
MA0028.10.0816
MA0029.10.4
MA0030.10.419
MA0031.10.661
MA0035.20.198
MA0038.10.0613
MA0039.20.338
MA0040.10.0786
MA0041.10.406
MA0042.10.914
MA0043.10.239
MA0046.10.0239
MA0047.20.577
MA0048.10.358
MA0050.10.712
MA0051.10.165
MA0052.10.325
MA0055.10.122
MA0057.10.844
MA0058.10.0268
MA0059.10.0734
MA0060.14.04367e-7
MA0061.10.0735
MA0062.20.834
MA0065.20.383
MA0066.10.766
MA0067.10.207
MA0068.10.51
MA0069.10.26
MA0070.10.466
MA0071.10.964
MA0072.10.934
MA0073.10.846
MA0074.10.252
MA0076.10.262
MA0077.10.234
MA0078.10.99
MA0079.20.481
MA0080.23.8705e-5
MA0081.10.199
MA0083.10.429
MA0084.10.0755
MA0087.10.615
MA0088.10.462
MA0090.10.0068
MA0091.10.203
MA0092.10.841
MA0093.10.0445
MA0099.27.56807e-14
MA0100.10.063
MA0101.10.00348
MA0102.20.351
MA0103.10.00493
MA0104.20.459
MA0105.10.257
MA0106.10.00119
MA0107.10.00155
MA0108.20.164
MA0111.10.0354
MA0112.20.0439
MA0113.10.411
MA0114.10.448
MA0115.10.157
MA0116.10.905
MA0117.10.861
MA0119.10.509
MA0122.10.964
MA0124.10.0346
MA0125.10.14
MA0131.10.476
MA0135.10.32
MA0136.16.57061e-5
MA0137.20.086
MA0138.20.652
MA0139.10.281
MA0140.10.577
MA0141.10.663
MA0142.10.067
MA0143.10.6
MA0144.10.0173
MA0145.10.612
MA0146.10.931
MA0147.10.732
MA0148.10.908
MA0149.10.604
MA0150.11.68396e-7
MA0152.10.0121
MA0153.10.976
MA0154.10.66
MA0155.10.344
MA0156.10.0346
MA0157.10.934
MA0159.10.212
MA0160.10.701
MA0162.10.0352
MA0163.10.0793
MA0164.10.319
MA0258.10.591
MA0259.10.948



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: CNhs12368

Novel motifP-value
10.965
100.335
1000.988
1010.661
1020.585
1030.109
1040.753
1050.66
1060.438
1070.621
1080.174
1090.0592
110.474
1100.334
1110.673
1120.105
1138.96369e-4
1140.374
1150.619
1160.0515
1170.0373
1180.713
1190.729
120.932
1200.11
1210.624
1220.0811
1238.28523e-4
1240.0465
1250.916
1260.903
1270.817
1280.936
1290.214
130.415
1300.567
1310.133
1320.401
1330.538
1340.569
1350.541
1360.229
1370.749
1380.943
1390.141
140.446
1400.721
1410.51
1420.749
1430.213
1440.534
1450.976
1460.952
1470.273
1480.909
1490.239
150.797
1500.17
1510.832
1520.0271
1530.448
1540.302
1550.00511
1560.163
1570.943
1580.065
1590.126
160.0452
1600.296
1610.333
1620.194
1630.556
1640.00988
1650.702
1660.357
1670.383
1680.855
1690.119
170.549
180.0228
190.132
20.797
200.326
210.52
220.142
230.24
240.87
250.0579
260.703
270.881
280.841
290.0674
30.696
300.973
310.535
322.40754e-5
330.669
340.646
350.89
360.0483
370.00161
380.24
390.251
40.023
400.407
410.989
420.397
430.669
440.943
450.861
460.837
470.558
480.857
490.118
50.888
500.876
510.611
520.947
530.00918
540.959
550.216
560.658
570.723
580.12
590.427
60.357
600.565
610.677
620.13
630.553
640.886
650.97
660.201
670.319
680.614
690.321
70.141
700.747
710.522
720.685
730.00154
740.0608
750.21
760.345
770.0109
780.018
790.509
80.517
800.663
810.8
820.958
830.758
840.857
850.159
860.19
870.00288
880.626
890.176
90.689
900.933
910.491
920.156
930.799
940.504
950.011
960.468
970.164
980.125
990.695



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: CNhs12368


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)
0000011 (migratory trunk neural crest cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000133 (neurectodermal cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000333 (migratory neural crest cell)
0000548 (animal cell)
0000569 (cardiac mesenchymal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002494 (cardiocyte)

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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