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FF:11531-120A1: 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 16:46, 29 March 2012


Name:Fibroblast - Conjunctival, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueeye
dev stageNA
sexNA
ageNA
cell typefibroblast
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 numberSC6575
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-0.167
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-lymphoma0.04
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
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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: CNhs11339

Jaspar motifP-value
MA0002.20.96
MA0003.10.288
MA0004.10.344
MA0006.10.497
MA0007.10.235
MA0009.10.147
MA0014.10.859
MA0017.10.956
MA0018.20.695
MA0019.10.676
MA0024.10.671
MA0025.10.85
MA0027.10.488
MA0028.10.284
MA0029.10.485
MA0030.10.792
MA0031.10.0953
MA0035.20.136
MA0038.10.00597
MA0039.20.804
MA0040.10.431
MA0041.10.273
MA0042.10.591
MA0043.10.707
MA0046.10.0686
MA0047.20.931
MA0048.10.181
MA0050.10.00491
MA0051.10.0793
MA0052.10.981
MA0055.13.32197e-4
MA0057.10.518
MA0058.10.926
MA0059.10.768
MA0060.14.34158e-6
MA0061.10.309
MA0062.20.26
MA0065.20.104
MA0066.10.997
MA0067.10.0167
MA0068.10.68
MA0069.10.947
MA0070.10.0323
MA0071.10.472
MA0072.10.737
MA0073.10.894
MA0074.10.426
MA0076.10.542
MA0077.10.321
MA0078.10.796
MA0079.20.694
MA0080.21.4577e-6
MA0081.10.191
MA0083.10.246
MA0084.10.158
MA0087.10.91
MA0088.10.29
MA0090.10.225
MA0091.10.205
MA0092.10.99
MA0093.10.537
MA0099.21.02781e-4
MA0100.10.917
MA0101.10.659
MA0102.20.333
MA0103.10.397
MA0104.20.619
MA0105.10.487
MA0106.10.149
MA0107.10.554
MA0108.20.0753
MA0111.10.174
MA0112.20.825
MA0113.10.0194
MA0114.10.24
MA0115.10.875
MA0116.10.744
MA0117.10.214
MA0119.10.466
MA0122.10.231
MA0124.10.0972
MA0125.10.534
MA0131.10.967
MA0135.10.0456
MA0136.11.98379e-4
MA0137.20.183
MA0138.20.963
MA0139.10.643
MA0140.10.0839
MA0141.10.474
MA0142.10.344
MA0143.10.268
MA0144.10.28
MA0145.10.513
MA0146.10.0645
MA0147.10.387
MA0148.10.901
MA0149.10.967
MA0150.10.779
MA0152.10.291
MA0153.10.317
MA0154.10.93
MA0155.10.0542
MA0156.10.0252
MA0157.10.299
MA0159.10.863
MA0160.10.852
MA0162.10.106
MA0163.10.173
MA0164.10.774
MA0258.10.896
MA0259.10.606



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: CNhs11339

Novel motifP-value
10.289
100.317
1000.753
1010.379
1020.375
1030.219
1040.118
1050.0276
1060.993
1070.207
1080.142
1090.0461
110.18
1100.0976
1110.421
1120.134
1130.0564
1140.319
1150.271
1160.147
1170.786
1180.768
1190.801
120.56
1200.906
1210.943
1220.424
1230.00409
1240.917
1250.777
1260.707
1270.787
1280.417
1290.834
130.996
1300.0504
1310.389
1320.572
1330.297
1340.171
1350.605
1360.885
1370.0616
1380.377
1390.168
140.678
1400.797
1410.264
1420.236
1430.761
1440.585
1450.482
1460.0386
1470.547
1480.671
1490.61
150.756
1500.324
1510.888
1520.0768
1530.623
1540.0159
1550.215
1560.2
1570.356
1580.0905
1590.512
160.788
1600.106
1610.511
1620.0241
1630.933
1640.888
1650.117
1660.574
1670.275
1680.385
1690.222
170.785
180.00426
190.126
20.721
200.966
210.675
220.242
230.55
240.662
250.193
260.407
270.973
280.0518
290.333
30.497
300.0518
310.556
320.0665
330.0584
340.132
350.717
360.78
370.272
380.75
390.479
40.573
400.105
410.346
420.905
430.449
440.0502
450.169
460.757
470.594
480.371
490.538
50.326
500.179
510.823
520.979
530.163
540.621
550.315
560.282
570.815
580.0899
590.185
60.716
600.887
610.392
620.061
630.575
640.117
650.275
660.017
670.387
680.0603
690.386
70.766
700.413
710.716
720.779
730.0186
740.729
750.933
760.517
770.187
780.289
790.554
80.347
800.494
810.752
820.23
830.477
840.301
850.965
860.702
870.107
880.143
890.725
90.148
900.0249
910.624
920.909
930.934
940.397
950.357
960.936
970.338
980.881
990.00395



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: CNhs11339


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)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002550 (fibroblast of the conjuctiva)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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