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FF:11936-126A1: 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 17:40, 29 March 2012


Name:Olfactory epithelial cells, donor4
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexmale
age64
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-penis0.0577
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-0.05
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs13819

Jaspar motifP-value
MA0002.20.0124
MA0003.10.78
MA0004.10.0276
MA0006.10.853
MA0007.10.396
MA0009.10.134
MA0014.10.186
MA0017.10.0665
MA0018.21.52805e-5
MA0019.10.238
MA0024.10.0147
MA0025.10.0529
MA0027.10.477
MA0028.16.78067e-5
MA0029.10.338
MA0030.10.0311
MA0031.10.0357
MA0035.20.00391
MA0038.10.03
MA0039.20.00615
MA0040.10.761
MA0041.10.958
MA0042.10.689
MA0043.11.70608e-4
MA0046.10.184
MA0047.20.185
MA0048.10.022
MA0050.10.945
MA0051.10.393
MA0052.10.0878
MA0055.10.592
MA0057.10.255
MA0058.11.69453e-4
MA0059.10.0988
MA0060.11.29544e-9
MA0061.10.0223
MA0062.23.19274e-15
MA0065.20.0557
MA0066.10.942
MA0067.18.5233e-5
MA0068.10.534
MA0069.10.0676
MA0070.10.475
MA0071.10.47
MA0072.10.107
MA0073.10.252
MA0074.10.514
MA0076.19.05675e-7
MA0077.10.627
MA0078.10.821
MA0079.20.477
MA0080.21.35206e-9
MA0081.13.68335e-4
MA0083.19.67047e-5
MA0084.10.0563
MA0087.10.804
MA0088.10.19
MA0090.17.80737e-8
MA0091.10.0588
MA0092.10.122
MA0093.10.011
MA0099.21.35566e-4
MA0100.10.45
MA0101.10.0102
MA0102.20.631
MA0103.10.00543
MA0104.20.00133
MA0105.10.00285
MA0106.10.0991
MA0107.10.0333
MA0108.20.772
MA0111.10.212
MA0112.20.973
MA0113.10.768
MA0114.10.0437
MA0115.10.0453
MA0116.10.0433
MA0117.10.00597
MA0119.10.00718
MA0122.10.451
MA0124.10.627
MA0125.10.946
MA0131.10.947
MA0135.10.6
MA0136.15.96202e-14
MA0137.20.231
MA0138.20.882
MA0139.10.437
MA0140.10.0176
MA0141.10.18
MA0142.10.521
MA0143.10.806
MA0144.10.645
MA0145.10.442
MA0146.10.761
MA0147.10.0167
MA0148.10.187
MA0149.10.795
MA0150.10.00345
MA0152.10.0189
MA0153.10.445
MA0154.10.0707
MA0155.10.623
MA0156.19.75483e-11
MA0157.10.158
MA0159.10.26
MA0160.10.00504
MA0162.10.108
MA0163.10.617
MA0164.10.726
MA0258.10.539
MA0259.10.695



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: CNhs13819

Novel motifP-value
10.262
100.877
1000.575
1010.629
1020.0208
1030.552
1040.801
1050.177
1060.919
1070.0825
1080.694
1090.703
110.623
1100.758
1110.398
1120.854
1130.352
1140.734
1150.343
1160.174
1170.491
1180.659
1190.612
120.154
1200.971
1210.493
1220.0997
1230.237
1240.344
1250.518
1260.0937
1270.747
1280.888
1290.539
130.0732
1300.814
1310.768
1320.0738
1330.967
1340.909
1350.98
1360.615
1370.138
1380.945
1390.287
140.463
1400.407
1410.0342
1420.534
1430.419
1440.996
1450.288
1460.328
1470.1
1480.524
1490.119
150.149
1500.684
1510.646
1520.425
1530.451
1540.898
1550.113
1560.297
1570.151
1580.0316
1590.927
160.322
1600.422
1610.897
1620.56
1630.257
1640.136
1650.483
1660.00165
1670.548
1680.304
1690.169
170.769
180.758
190.0123
20.632
200.84
210.306
220.699
230.299
240.139
250.26
260.644
270.924
280.413
290.668
30.833
300.375
310.645
322.13357e-15
330.401
340.789
350.428
360.0692
370.802
380.281
390.305
40.209
400.113
410.215
420.724
430.741
440.922
450.774
460.79
470.408
480.675
490.591
50.807
500.601
510.452
520.981
530.368
540.694
550.0213
560.985
570.748
580.209
590.537
60.912
600.469
610.304
620.845
630.471
640.248
650.879
660.0657
670.984
680.932
690.993
70.118
700.643
710.333
720.225
730.421
740.439
750.261
760.743
770.073
780.265
790.0018
80.537
800.0565
810.594
820.186
830.324
840.328
850.33
860.279
870.318
880.145
890.273
90.718
900.914
910.839
920.35
930.683
940.385
950.381
960.595
970.509
980.0408
990.00231



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: CNhs13819


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

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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