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FF:11616-122A5: 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 17:11, 29 March 2012


Name:Mesenchymal Stem Cells - bone marrow, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
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 numberSC7505
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-0.0244
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-lymphoma0.152
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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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: CNhs12100

Jaspar motifP-value
MA0002.20.243
MA0003.10.344
MA0004.10.586
MA0006.10.657
MA0007.10.00238
MA0009.10.0638
MA0014.10.9
MA0017.10.117
MA0018.20.00293
MA0019.10.774
MA0024.10.705
MA0025.10.114
MA0027.10.281
MA0028.10.421
MA0029.10.0394
MA0030.11.60618e-5
MA0031.18.99065e-6
MA0035.20.409
MA0038.10.0399
MA0039.20.787
MA0040.10.16
MA0041.10.494
MA0042.10.533
MA0043.14.08483e-5
MA0046.10.106
MA0047.20.183
MA0048.10.187
MA0050.11.61196e-11
MA0051.14.82727e-7
MA0052.10.0158
MA0055.10.11
MA0057.10.372
MA0058.10.848
MA0059.10.096
MA0060.10.00214
MA0061.10.339
MA0062.20.0177
MA0065.20.0672
MA0066.10.0212
MA0067.10.0398
MA0068.19.37233e-4
MA0069.10.811
MA0070.10.0455
MA0071.10.0353
MA0072.10.105
MA0073.10.772
MA0074.10.71
MA0076.10.0491
MA0077.10.762
MA0078.10.415
MA0079.20.181
MA0080.23.05086e-6
MA0081.10.0469
MA0083.10.0041
MA0084.10.439
MA0087.10.474
MA0088.10.181
MA0090.10.194
MA0091.10.234
MA0092.10.333
MA0093.10.761
MA0099.20.00174
MA0100.10.893
MA0101.10.74
MA0102.23.80166e-4
MA0103.10.441
MA0104.20.379
MA0105.10.0191
MA0106.10.0834
MA0107.10.785
MA0108.20.00313
MA0111.10.703
MA0112.25.16574e-4
MA0113.10.0135
MA0114.10.0554
MA0115.10.889
MA0116.10.0233
MA0117.10.921
MA0119.10.0223
MA0122.10.505
MA0124.10.498
MA0125.10.131
MA0131.10.566
MA0135.10.0362
MA0136.11.1045e-5
MA0137.29.61317e-4
MA0138.20.0724
MA0139.10.585
MA0140.10.158
MA0141.10.00921
MA0142.10.401
MA0143.10.898
MA0144.10.307
MA0145.10.527
MA0146.10.0407
MA0147.10.153
MA0148.10.799
MA0149.10.0464
MA0150.10.734
MA0152.10.437
MA0153.10.812
MA0154.10.115
MA0155.10.149
MA0156.10.00238
MA0157.10.0864
MA0159.10.404
MA0160.10.0366
MA0162.10.237
MA0163.10.00126
MA0164.10.659
MA0258.10.0172
MA0259.10.511



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: CNhs12100

Novel motifP-value
10.133
100.358
1000.395
1010.536
1020.548
1030.264
1040.401
1050.123
1060.111
1070.125
1080.537
1090.0284
110.0119
1100.0609
1110.12
1120.252
1130.569
1140.243
1150.976
1160.135
1170.404
1180.39
1190.257
120.916
1200.0783
1210.963
1220.999
1230.915
1240.672
1250.139
1260.58
1270.0661
1280.21
1290.586
130.32
1300.768
1310.621
1320.338
1330.449
1340.831
1350.583
1360.646
1370.197
1380.203
1390.374
140.982
1400.335
1410.293
1420.272
1430.0807
1440.759
1450.098
1460.662
1470.438
1480.818
1490.189
150.165
1500.35
1510.454
1520.206
1530.916
1540.746
1550.749
1560.236
1570.753
1580.912
1590.715
160.23
1600.0026
1610.938
1620.311
1630.396
1640.66
1650.717
1660.731
1670.538
1680.796
1690.0401
170.18
180.0801
190.111
20.673
200.898
210.514
220.161
230.247
240.819
250.79
260.0112
270.258
280.481
290.217
30.226
300.578
310.427
324.8488e-4
330.239
340.678
350.688
360.055
370.151
380.232
390.542
40.409
400.0176
410.757
420.488
430.142
440.377
450.6
460.0103
470.11
480.1
490.0902
50.589
500.596
510.326
520.899
530.993
540.339
550.343
560.252
570.0675
580.898
590.0451
60.946
600.582
610.573
620.406
630.165
640.101
650.0554
660.0483
670.888
680.377
690.00779
70.578
700.342
710.0534
720.745
730.0915
740.869
750.256
760.872
770.183
780.334
790.143
80.00854
800.847
810.335
820.191
830.502
840.37
850.228
860.845
870.503
880.377
890.113
90.443
900.702
910.329
920.275
930.211
940.0876
950.0823
960.28
970.746
980.093
990.00863



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: CNhs12100


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)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002092 (bone marrow cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002540 (mesenchymal stem cell of the bone marrow)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical 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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