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FF:11571-120E5: 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 17:10, 29 March 2012


Name:Pericytes, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexNA
ageNA
cell typepericyte
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 numberSC1205
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-0.012
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-0.445
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: CNhs12079

Jaspar motifP-value
MA0002.20.759
MA0003.10.193
MA0004.10.839
MA0006.10.363
MA0007.10.214
MA0009.10.268
MA0014.10.542
MA0017.10.375
MA0018.20.0826
MA0019.10.0363
MA0024.10.00121
MA0025.10.42
MA0027.10.524
MA0028.10.0202
MA0029.10.43
MA0030.10.559
MA0031.10.0716
MA0035.20.78
MA0038.10.513
MA0039.20.796
MA0040.10.281
MA0041.10.211
MA0042.10.467
MA0043.10.00342
MA0046.10.259
MA0047.20.347
MA0048.10.628
MA0050.10.00362
MA0051.10.00322
MA0052.10.00135
MA0055.10.887
MA0057.10.595
MA0058.10.904
MA0059.10.61
MA0060.10.711
MA0061.10.862
MA0062.25.67473e-6
MA0065.20.205
MA0066.10.136
MA0067.10.062
MA0068.10.328
MA0069.10.186
MA0070.10.0563
MA0071.10.0364
MA0072.10.479
MA0073.10.869
MA0074.10.368
MA0076.10.00268
MA0077.10.257
MA0078.10.643
MA0079.20.316
MA0080.26.65974e-8
MA0081.10.015
MA0083.14.89071e-4
MA0084.10.942
MA0087.10.566
MA0088.10.614
MA0090.10.0307
MA0091.11.21064e-5
MA0092.10.851
MA0093.10.925
MA0099.20.0236
MA0100.10.104
MA0101.10.0845
MA0102.27.81094e-4
MA0103.10.915
MA0104.20.332
MA0105.10.963
MA0106.10.815
MA0107.10.207
MA0108.26.9081e-10
MA0111.10.285
MA0112.20.0118
MA0113.10.0345
MA0114.10.347
MA0115.10.606
MA0116.10.843
MA0117.10.125
MA0119.10.457
MA0122.10.575
MA0124.10.628
MA0125.10.911
MA0131.10.24
MA0135.10.0377
MA0136.13.40761e-12
MA0137.20.154
MA0138.20.16
MA0139.10.75
MA0140.10.342
MA0141.10.0472
MA0142.10.217
MA0143.10.786
MA0144.10.508
MA0145.10.27
MA0146.10.0126
MA0147.10.331
MA0148.10.303
MA0149.10.0948
MA0150.10.0684
MA0152.10.598
MA0153.10.229
MA0154.10.16
MA0155.10.0147
MA0156.17.29133e-11
MA0157.10.0826
MA0159.10.619
MA0160.10.542
MA0162.10.139
MA0163.10.226
MA0164.10.372
MA0258.10.0171
MA0259.10.553



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: CNhs12079

Novel motifP-value
10.607
100.121
1000.994
1010.529
1020.894
1030.932
1040.222
1050.262
1060.219
1070.0828
1080.328
1090.123
110.148
1100.181
1110.809
1120.942
1130.0026
1140.543
1150.11
1160.149
1170.96
1180.926
1190.928
120.835
1200.11
1210.716
1220.0791
1233.91275e-4
1240.631
1250.158
1260.723
1270.934
1280.309
1290.583
130.893
1300.667
1310.948
1320.11
1330.814
1340.0858
1350.866
1360.661
1370.03
1380.591
1390.262
140.929
1400.745
1410.256
1420.67
1430.699
1440.379
1450.549
1460.331
1470.116
1480.397
1490.0683
150.26
1500.487
1510.687
1520.161
1530.303
1540.0762
1550.712
1560.706
1570.574
1580.998
1590.536
160.131
1600.0939
1610.749
1620.0883
1630.552
1640.381
1650.125
1660.701
1670.0752
1680.949
1690.0478
170.286
180.36
190.0529
20.124
200.642
210.816
220.0537
230.29
240.551
250.559
260.236
270.291
280.185
290.902
30.932
300.0663
310.36
327.74013e-11
330.882
340.0937
350.916
360.189
370.36
380.458
390.467
40.852
400.335
410.337
420.877
430.417
440.116
450.17
460.382
470.739
480.388
490.493
50.539
500.386
510.393
520.449
530.414
540.393
550.897
560.32
570.623
580.34
590.0102
60.395
600.442
610.92
620.63
630.541
640.397
650.0412
660.551
670.929
680.0519
690.0932
70.915
700.318
710.707
720.343
730.0989
740.14
750.899
760.291
770.0196
780.945
790.00178
80.229
800.615
810.675
820.107
830.5
840.271
850.0459
860.961
870.822
880.535
890.0807
90.0649
900.0169
910.365
920.764
930.734
940.729
950.389
960.688
970.481
980.298
990.0147



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: CNhs12079


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)
0000183 (contractile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000630 (supportive cell)
0000669 (pericyte cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002575 (central nervous system pericyte)

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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