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FF:11313-117C8: 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 17:00, 29 March 2012


Name:Macrophage - monocyte derived, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stage46 years old adult
sexmale
age46
cell typemacrophage
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberMac723
catalog number3H100-80-10
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-0.176
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-0.00284
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: CNhs11899

Jaspar motifP-value
MA0002.22.10745e-4
MA0003.10.0558
MA0004.10.444
MA0006.10.426
MA0007.10.108
MA0009.10.583
MA0014.10.104
MA0017.11.37984e-4
MA0018.20.0113
MA0019.10.989
MA0024.10.0901
MA0025.10.826
MA0027.10.513
MA0028.10.735
MA0029.10.839
MA0030.10.00312
MA0031.10.0664
MA0035.20.979
MA0038.10.458
MA0039.20.0195
MA0040.10.88
MA0041.10.504
MA0042.10.958
MA0043.10.33
MA0046.10.38
MA0047.20.539
MA0048.10.398
MA0050.13.8559e-4
MA0051.10.00862
MA0052.10.402
MA0055.10.815
MA0057.10.367
MA0058.10.0572
MA0059.10.0644
MA0060.12.79454e-4
MA0061.10.0311
MA0062.20.00213
MA0065.23.80679e-4
MA0066.10.0834
MA0067.10.309
MA0068.16.84825e-5
MA0069.10.193
MA0070.10.457
MA0071.10.082
MA0072.10.461
MA0073.10.287
MA0074.10.28
MA0076.10.575
MA0077.10.279
MA0078.10.795
MA0079.20.535
MA0080.28.24428e-16
MA0081.13.33849e-4
MA0083.10.387
MA0084.10.0209
MA0087.10.425
MA0088.10.148
MA0090.10.0478
MA0091.10.133
MA0092.10.0894
MA0093.10.282
MA0099.21.44649e-4
MA0100.10.963
MA0101.10.253
MA0102.20.199
MA0103.10.543
MA0104.20.412
MA0105.10.00696
MA0106.10.431
MA0107.10.129
MA0108.20.0014
MA0111.10.322
MA0112.24.29188e-5
MA0113.10.263
MA0114.10.00257
MA0115.10.391
MA0116.16.3713e-4
MA0117.10.98
MA0119.10.885
MA0122.10.198
MA0124.10.0553
MA0125.10.88
MA0131.10.471
MA0135.10.431
MA0136.13.24167e-12
MA0137.20.614
MA0138.20.918
MA0139.10.434
MA0140.10.93
MA0141.10.00248
MA0142.10.546
MA0143.10.27
MA0144.10.099
MA0145.10.0575
MA0146.10.0195
MA0147.10.55
MA0148.10.768
MA0149.10.0993
MA0150.10.0109
MA0152.10.259
MA0153.10.00679
MA0154.10.00429
MA0155.10.882
MA0156.11.66822e-6
MA0157.10.251
MA0159.10.00675
MA0160.10.003
MA0162.10.971
MA0163.17.2795e-4
MA0164.10.907
MA0258.10.00626
MA0259.10.522



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: CNhs11899

Novel motifP-value
10.0393
100.0393
1000.942
1010.534
1020.465
1030.11
1040.373
1050.684
1060.106
1070.477
1080.877
1090.00362
110.0737
1100.12
1110.0113
1120.0653
1130.626
1140.0226
1150.486
1160.535
1170.0401
1180.285
1190.11
120.553
1200.823
1210.859
1220.419
1230.682
1240.417
1250.147
1260.268
1270.118
1280.108
1290.294
130.0289
1300.494
1310.7
1320.805
1330.449
1340.873
1350.114
1360.301
1370.0285
1380.387
1390.139
140.327
1400.74
1410.557
1420.65
1430.295
1440.602
1450.511
1460.927
1470.429
1480.0157
1490.523
150.079
1500.663
1510.727
1520.0764
1530.9
1540.959
1550.574
1560.595
1570.745
1580.433
1590.261
160.144
1600.464
1610.644
1620.39
1630.808
1640.257
1650.326
1660.884
1670.614
1680.486
1690.00262
170.184
180.205
190.211
20.81
200.935
210.267
220.118
230.201
240.014
250.438
260.133
270.252
280.342
290.346
30.071
300.945
310.792
320.864
330.232
340.306
350.738
360.148
370.127
380.067
390.868
40.688
400.0598
410.0273
420.651
430.0804
440.0777
450.61
460.212
470.248
480.343
490.232
50.281
500.922
510.549
520.364
530.415
540.353
550.0817
560.564
570.757
580.0987
590.0753
60.381
600.117
610.369
620.0502
630.442
640.321
650.0605
660.958
670.301
680.162
690.67
70.136
700.0904
710.0349
720.241
730.0137
740.917
750.0827
760.42
770.248
780.0673
790.785
80.19
800.312
810.272
820.215
830.27
840.648
850.0394
860.116
870.0304
880.295
890.0552
90.269
900.04
910.861
920.18
930.617
940.12
950.0661
960.149
970.84
980.604
990.691



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: CNhs11899


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)
0000037 (hematopoietic stem cell)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000235 (macrophage)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002194 (monopoietic cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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