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FF:11493-119E8: 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 16:44, 29 March 2012


Name:Meningeal Cells, donor1
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 numberNA
catalog numberSC1405
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-0.191
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-lymphoma0.292
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: CNhs11320

Jaspar motifP-value
MA0002.20.811
MA0003.10.7
MA0004.10.457
MA0006.10.302
MA0007.10.101
MA0009.10.437
MA0014.10.945
MA0017.10.926
MA0018.20.0684
MA0019.10.299
MA0024.11.92501e-6
MA0025.10.312
MA0027.10.498
MA0028.10.197
MA0029.10.694
MA0030.10.433
MA0031.10.219
MA0035.20.464
MA0038.12.37812e-4
MA0039.20.0783
MA0040.10.195
MA0041.10.24
MA0042.10.413
MA0043.10.0456
MA0046.10.0234
MA0047.20.32
MA0048.10.103
MA0050.12.51615e-7
MA0051.10.00247
MA0052.10.102
MA0055.10.00887
MA0057.10.598
MA0058.10.686
MA0059.10.574
MA0060.19.23801e-15
MA0061.10.0186
MA0062.20.881
MA0065.20.302
MA0066.10.826
MA0067.10.00101
MA0068.10.517
MA0069.10.631
MA0070.10.0169
MA0071.10.81
MA0072.10.973
MA0073.10.971
MA0074.10.547
MA0076.10.439
MA0077.10.266
MA0078.10.735
MA0079.20.68
MA0080.20.0898
MA0081.10.888
MA0083.17.51698e-4
MA0084.10.88
MA0087.10.547
MA0088.10.202
MA0090.14.48243e-4
MA0091.10.645
MA0092.10.82
MA0093.10.463
MA0099.21.2176e-7
MA0100.10.228
MA0101.10.401
MA0102.29.04985e-4
MA0103.16.08167e-4
MA0104.20.962
MA0105.10.0601
MA0106.10.525
MA0107.10.128
MA0108.20.00932
MA0111.10.129
MA0112.20.511
MA0113.10.254
MA0114.10.696
MA0115.10.559
MA0116.10.275
MA0117.10.33
MA0119.10.7
MA0122.10.585
MA0124.10.166
MA0125.10.496
MA0131.10.918
MA0135.10.157
MA0136.10.306
MA0137.20.858
MA0138.20.106
MA0139.10.835
MA0140.10.326
MA0141.10.734
MA0142.10.243
MA0143.10.563
MA0144.10.893
MA0145.10.826
MA0146.10.116
MA0147.10.972
MA0148.10.187
MA0149.10.763
MA0150.10.841
MA0152.10.842
MA0153.10.528
MA0154.10.914
MA0155.10.382
MA0156.10.567
MA0157.10.401
MA0159.10.115
MA0160.10.816
MA0162.10.117
MA0163.10.236
MA0164.10.959
MA0258.10.118
MA0259.10.839



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: CNhs11320

Novel motifP-value
10.0781
100.0187
1000.75
1010.585
1020.204
1030.194
1040.797
1050.0584
1060.206
1070.75
1080.266
1090.529
110.862
1100.179
1110.572
1120.171
1130.234
1140.461
1150.174
1160.922
1170.681
1180.0767
1190.719
120.604
1200.968
1210.572
1220.999
1233.33425e-4
1240.71
1250.191
1260.363
1270.572
1280.243
1290.409
130.877
1300.00994
1310.518
1320.836
1330.769
1340.121
1350.832
1360.902
1370.1
1380.497
1390.00398
140.451
1400.698
1410.807
1420.904
1430.505
1440.305
1450.777
1460.0243
1470.381
1480.0636
1490.585
150.478
1500.286
1510.235
1520.952
1530.482
1540.0295
1550.0607
1560.766
1570.298
1580.103
1590.734
160.559
1600.267
1610.935
1620.356
1630.455
1640.0114
1650.0962
1660.575
1670.0614
1680.93
1690.252
170.891
180.72
190.303
20.628
200.499
210.86
220.135
230.632
240.255
250.578
260.817
270.424
280.24
290.193
30.216
300.0311
310.448
320.582
330.309
340.171
350.0693
360.958
370.288
380.71
390.44
40.871
400.143
410.991
420.905
430.267
440.0875
450.354
460.5
470.954
480.86
490.375
50.381
500.278
510.831
520.511
530.164
540.93
550.459
560.749
570.879
580.0509
590.197
60.393
600.302
610.928
620.0636
630.44
640.954
650.654
660.00888
670.288
680.432
690.767
70.936
700.0149
710.251
720.101
730.998
740.984
750.195
760.201
770.449
780.783
790.522
80.985
800.357
810.0535
820.00516
830.698
840.0161
850.134
860.232
870.296
880.474
890.96
90.119
900.0509
910.23
920.159
930.887
940.97
950.592
960.286
970.118
980.462
990.00278



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: CNhs11320


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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