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FF:11389-118C3: 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 17:06, 29 March 2012


Name:Macrophage - monocyte derived, donor3
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 stage57 years old adult
sexfemale
age57
cell typemacrophage
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberMac724
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-0.0579
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0663
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.181
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs12003

Jaspar motifP-value
MA0002.20.00129
MA0003.10.105
MA0004.10.321
MA0006.10.328
MA0007.10.027
MA0009.10.674
MA0014.10.0631
MA0017.12.64892e-4
MA0018.20.00324
MA0019.10.453
MA0024.10.247
MA0025.10.992
MA0027.10.828
MA0028.10.906
MA0029.10.882
MA0030.10.00235
MA0031.10.0417
MA0035.20.655
MA0038.10.445
MA0039.20.0163
MA0040.10.88
MA0041.10.288
MA0042.10.562
MA0043.10.0488
MA0046.10.463
MA0047.20.62
MA0048.10.319
MA0050.13.85709e-4
MA0051.10.0213
MA0052.10.263
MA0055.10.961
MA0057.10.311
MA0058.10.0307
MA0059.10.167
MA0060.10.0165
MA0061.10.209
MA0062.20.00302
MA0065.20.00292
MA0066.10.163
MA0067.10.483
MA0068.10.00443
MA0069.10.19
MA0070.10.56
MA0071.10.0982
MA0072.10.778
MA0073.10.138
MA0074.10.0907
MA0076.10.957
MA0077.10.669
MA0078.10.617
MA0079.20.0579
MA0080.29.78276e-17
MA0081.14.45831e-4
MA0083.10.0318
MA0084.10.0253
MA0087.10.681
MA0088.10.144
MA0090.10.0142
MA0091.10.132
MA0092.10.171
MA0093.10.194
MA0099.20.1
MA0100.10.711
MA0101.10.774
MA0102.20.217
MA0103.10.709
MA0104.20.663
MA0105.10.14
MA0106.10.502
MA0107.10.581
MA0108.20.00646
MA0111.10.23
MA0112.27.7328e-4
MA0113.10.356
MA0114.10.00365
MA0115.10.256
MA0116.10.00167
MA0117.10.824
MA0119.10.753
MA0122.10.46
MA0124.10.312
MA0125.10.614
MA0131.10.253
MA0135.10.0614
MA0136.15.15171e-12
MA0137.20.269
MA0138.20.72
MA0139.10.942
MA0140.10.421
MA0141.10.00407
MA0142.10.579
MA0143.10.249
MA0144.10.0483
MA0145.10.0776
MA0146.10.00443
MA0147.10.951
MA0148.10.252
MA0149.10.124
MA0150.10.0611
MA0152.10.143
MA0153.10.00598
MA0154.10.0112
MA0155.10.712
MA0156.12.43781e-7
MA0157.10.318
MA0159.10.0197
MA0160.10.00348
MA0162.10.967
MA0163.10.00916
MA0164.10.775
MA0258.10.0104
MA0259.10.307



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: CNhs12003

Novel motifP-value
10.114
100.0414
1000.865
1010.28
1020.25
1030.16
1040.491
1050.808
1060.0768
1070.332
1080.759
1090.0057
110.0901
1100.226
1110.0302
1120.111
1130.416
1140.0617
1150.712
1160.514
1170.0415
1180.245
1190.188
120.5
1200.538
1210.594
1220.553
1230.72
1240.631
1250.0604
1260.189
1270.0863
1280.093
1290.541
130.0238
1300.802
1310.695
1320.63
1330.925
1340.561
1350.162
1360.159
1370.0169
1380.288
1390.144
140.387
1400.401
1410.516
1420.373
1430.469
1440.376
1450.681
1460.977
1470.135
1480.0633
1490.405
150.137
1500.42
1510.724
1520.0227
1530.217
1540.979
1550.142
1560.421
1570.785
1580.995
1590.367
160.127
1600.542
1610.666
1620.781
1630.679
1640.137
1650.386
1660.599
1670.565
1680.7
1690.00491
170.166
180.31
190.15
20.809
200.867
210.141
220.0991
230.368
240.0166
250.575
260.0159
270.121
280.557
290.127
30.0545
300.831
310.737
320.729
330.382
340.178
350.917
360.386
370.147
380.0744
390.973
40.689
400.117
410.172
420.772
430.107
440.0034
450.722
460.187
470.394
480.24
490.311
50.761
500.922
510.567
520.283
530.353
540.373
550.164
560.701
570.9
580.162
590.0751
60.105
600.119
610.217
620.0935
630.537
640.252
650.0562
660.946
670.292
680.993
690.466
70.275
700.086
710.0564
720.332
730.00288
740.706
750.0327
760.616
770.178
780.0669
790.199
80.12
800.378
810.258
820.394
830.95
840.476
850.0249
860.0951
870.00767
880.262
890.113
90.16
900.115
910.724
920.247
930.89
940.249
950.0272
960.247
970.955
980.501
990.886



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: CNhs12003


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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