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FF:11654-122E7: 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 17:24, 29 March 2012


Name:Meningeal Cells, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuemeninges
dev stageNA
sexNA
ageNA
cell typemeningeal cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number4055
catalog numberSC1405
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-0.172
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-lymphoma0.634
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
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: CNhs12731

Jaspar motifP-value
MA0002.20.538
MA0003.10.183
MA0004.10.503
MA0006.10.297
MA0007.10.251
MA0009.10.915
MA0014.10.937
MA0017.10.744
MA0018.20.00157
MA0019.10.414
MA0024.11.69776e-16
MA0025.10.0564
MA0027.10.784
MA0028.10.00483
MA0029.10.672
MA0030.10.00896
MA0031.10.0544
MA0035.20.179
MA0038.10.0059
MA0039.20.542
MA0040.10.974
MA0041.10.766
MA0042.10.722
MA0043.13.2894e-4
MA0046.10.642
MA0047.20.817
MA0048.10.0236
MA0050.12.76139e-8
MA0051.10.0032
MA0052.10.499
MA0055.10.262
MA0057.10.695
MA0058.10.321
MA0059.10.554
MA0060.19.39292e-9
MA0061.10.00238
MA0062.20.893
MA0065.20.773
MA0066.10.246
MA0067.10.00205
MA0068.10.925
MA0069.10.714
MA0070.10.28
MA0071.10.623
MA0072.10.375
MA0073.10.922
MA0074.10.715
MA0076.10.142
MA0077.10.932
MA0078.10.815
MA0079.20.0328
MA0080.20.00195
MA0081.10.921
MA0083.10.0139
MA0084.10.0403
MA0087.10.48
MA0088.10.00424
MA0090.10.00374
MA0091.10.715
MA0092.10.975
MA0093.10.538
MA0099.21.57755e-5
MA0100.10.0138
MA0101.10.00752
MA0102.24.43263e-4
MA0103.11.34118e-5
MA0104.20.766
MA0105.10.393
MA0106.10.44
MA0107.12.24772e-4
MA0108.20.718
MA0111.10.549
MA0112.20.931
MA0113.10.954
MA0114.10.548
MA0115.10.705
MA0116.10.204
MA0117.10.91
MA0119.10.362
MA0122.10.686
MA0124.10.274
MA0125.10.878
MA0131.10.678
MA0135.10.238
MA0136.10.0528
MA0137.20.385
MA0138.20.116
MA0139.10.832
MA0140.10.816
MA0141.10.797
MA0142.10.459
MA0143.10.928
MA0144.10.588
MA0145.10.71
MA0146.10.598
MA0147.10.515
MA0148.10.507
MA0149.10.593
MA0150.10.259
MA0152.10.0331
MA0153.10.298
MA0154.10.634
MA0155.10.686
MA0156.10.932
MA0157.10.569
MA0159.10.263
MA0160.10.074
MA0162.10.0469
MA0163.10.222
MA0164.10.663
MA0258.10.0831
MA0259.10.0638



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: CNhs12731

Novel motifP-value
10.996
100.565
1000.938
1010.757
1020.206
1030.885
1040.669
1050.681
1060.169
1070.302
1080.348
1090.151
110.868
1100.202
1110.682
1120.205
1130.0348
1140.993
1150.663
1160.487
1170.575
1180.219
1190.535
120.354
1200.147
1210.53
1220.498
1237.60717e-4
1240.949
1250.323
1260.391
1270.329
1280.254
1290.824
130.241
1300.00788
1310.818
1320.641
1330.99
1340.277
1350.326
1360.158
1370.207
1380.452
1394.93403e-4
140.0515
1400.361
1410.831
1420.476
1430.257
1440.497
1450.871
1460.147
1470.275
1480.806
1490.954
150.886
1500.284
1510.134
1520.25
1530.814
1540.253
1550.0754
1560.62
1570.0716
1580.0107
1590.251
160.436
1600.0842
1610.55
1620.424
1630.97
1640.158
1650.46
1660.937
1670.289
1680.443
1690.148
170.845
180.493
190.236
20.981
200.39
210.0766
220.411
230.191
240.0315
250.862
260.643
270.451
280.323
290.757
30.764
300.496
310.37
320.351
330.155
340.893
350.164
360.156
370.966
380.735
390.491
40.466
400.644
410.462
420.405
430.42
440.831
450.346
460.915
470.319
480.61
490.181
50.63
500.616
510.912
520.112
530.119
540.766
550.589
560.939
570.739
580.127
590.286
60.948
600.0554
610.83
620.426
630.499
640.743
650.365
660.011
670.759
680.528
690.607
70.942
700.00891
710.72
720.55
730.908
740.638
750.93
760.481
770.952
780.754
790.84
80.359
800.798
810.321
820.017
830.21
840.208
850.0551
860.161
870.0521
880.64
890.905
90.368
900.748
910.761
920.0565
930.554
940.745
950.0954
960.606
970.289
980.778
990.00106



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: CNhs12731


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)
0000151 (secretory cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000327 (extracellular matrix secreting cell)
0000499 (stromal cell)
0000548 (animal cell)
0000708 (leptomeningeal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)
0003210 (blood-cerebrospinal fluid barrier)

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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