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FF:11572-120E6: 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 17:17, 29 March 2012


Name:Fibroblast - Choroid Plexus, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuechoroid plexus
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 numberSC1325
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-0.103
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-0.332
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12344

Jaspar motifP-value
MA0002.20.229
MA0003.10.915
MA0004.10.36
MA0006.10.201
MA0007.10.234
MA0009.10.307
MA0014.10.0483
MA0017.10.495
MA0018.21.97588e-6
MA0019.10.784
MA0024.18.98467e-5
MA0025.10.0239
MA0027.10.919
MA0028.14.04474e-4
MA0029.10.383
MA0030.10.306
MA0031.10.451
MA0035.20.51
MA0038.10.456
MA0039.20.00152
MA0040.10.48
MA0041.10.336
MA0042.10.539
MA0043.11.69918e-4
MA0046.10.49
MA0047.20.869
MA0048.10.79
MA0050.10.00373
MA0051.10.0125
MA0052.16.34368e-4
MA0055.10.0461
MA0057.10.876
MA0058.10.047
MA0059.10.1
MA0060.11.96776e-5
MA0061.10.145
MA0062.21.30767e-11
MA0065.20.0954
MA0066.10.646
MA0067.11.29306e-4
MA0068.10.113
MA0069.10.253
MA0070.10.268
MA0071.10.406
MA0072.10.888
MA0073.10.131
MA0074.10.886
MA0076.16.38154e-7
MA0077.10.563
MA0078.10.405
MA0079.20.262
MA0080.27.48648e-9
MA0081.10.0197
MA0083.10.256
MA0084.10.0539
MA0087.10.154
MA0088.10.0826
MA0090.10.0191
MA0091.13.96551e-4
MA0092.10.3
MA0093.10.237
MA0099.20.0192
MA0100.10.565
MA0101.10.0107
MA0102.20.049
MA0103.10.00633
MA0104.20.0112
MA0105.10.541
MA0106.10.932
MA0107.10.00614
MA0108.20.602
MA0111.10.543
MA0112.20.378
MA0113.10.019
MA0114.10.188
MA0115.10.0936
MA0116.10.791
MA0117.10.109
MA0119.10.133
MA0122.10.843
MA0124.10.857
MA0125.10.979
MA0131.10.456
MA0135.10.437
MA0136.16.87831e-10
MA0137.20.775
MA0138.20.861
MA0139.10.883
MA0140.10.811
MA0141.10.977
MA0142.10.31
MA0143.10.0201
MA0144.10.294
MA0145.10.586
MA0146.10.769
MA0147.10.0436
MA0148.10.835
MA0149.10.06
MA0150.10.0299
MA0152.10.0718
MA0153.10.173
MA0154.10.694
MA0155.10.278
MA0156.14.80272e-10
MA0157.10.897
MA0159.10.105
MA0160.10.0789
MA0162.10.169
MA0163.10.429
MA0164.10.819
MA0258.10.868
MA0259.10.498



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: CNhs12344

Novel motifP-value
10.117
100.122
1000.332
1010.721
1020.04
1030.0959
1040.391
1050.35
1060.0674
1070.0114
1080.441
1090.459
110.777
1100.714
1110.175
1120.455
1130.00884
1140.527
1150.371
1160.117
1170.655
1180.3
1190.629
120.0605
1200.041
1210.239
1226.78954e-4
1234.94644e-4
1240.718
1250.404
1260.87
1270.592
1280.171
1290.584
130.132
1300.621
1310.609
1320.401
1330.727
1340.732
1350.522
1360.275
1370.0708
1380.651
1390.425
140.493
1400.844
1410.834
1420.599
1430.415
1440.272
1450.36
1460.459
1470.0738
1480.707
1490.177
150.948
1500.201
1510.807
1520.851
1530.441
1540.154
1550.072
1560.243
1570.514
1580.592
1590.789
160.168
1600.325
1610.859
1620.179
1630.599
1640.944
1650.889
1660.254
1670.0943
1680.962
1690.173
170.709
180.169
190.0296
20.406
200.493
210.388
220.192
230.124
240.419
250.184
260.853
270.485
280.142
290.845
30.7
300.248
310.559
327.56546e-10
330.312
340.541
350.41
360.0292
370.962
380.866
390.422
40.37
400.0214
410.648
420.92
430.652
440.187
450.372
460.597
470.816
480.812
490.666
50.429
500.93
510.842
520.872
530.0612
540.811
550.262
560.907
570.701
580.2
590.124
60.459
600.874
610.374
620.787
630.741
640.638
650.35
660.513
670.944
680.144
690.13
70.581
700.168
710.978
720.639
730.938
740.606
750.59
760.905
770.283
780.649
790.0112
80.291
800.954
810.477
820.377
830.617
840.175
850.0186
860.991
870.0851
880.537
890.0871
90.212
900.463
910.175
920.329
930.546
940.388
950.184
960.629
970.701
980.785
990.00172



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: CNhs12344


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)
0002549 (fibroblast of choroid plexus)

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001009 (circulatory system)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0001886 (choroid plexus)
0002049 (vasculature)
0002050 (embryonic structure)
0002200 (vasculature of head)
0002384 (connective tissue)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0003947 (brain ventricle/choroid plexus)
0004086 (brain ventricle)
0004121 (ectoderm-derived structure)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0005281 (ventricular system of central nervous system)
0005282 (ventricular system of brain)
0005284 (brain vasculature)
0005358 (ventricle of nervous system)
0005423 (developing anatomical structure)
0005629 (vascular plexus)
0007798 (vascular system)

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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