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FF:11232-116C8: 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 16:35, 29 March 2012


Name:Macrophage - monocyte derived, donor1
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 stage65 years old adult
sexmale
age65
cell typemacrophage
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberMac722
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-0.148
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-0.136
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: CNhs10861

Jaspar motifP-value
MA0002.25.99139e-4
MA0003.10.149
MA0004.10.168
MA0006.10.597
MA0007.10.0916
MA0009.10.453
MA0014.10.115
MA0017.10.00118
MA0018.29.25952e-4
MA0019.10.502
MA0024.10.025
MA0025.10.834
MA0027.10.607
MA0028.10.661
MA0029.10.597
MA0030.10.0612
MA0031.10.423
MA0035.20.576
MA0038.10.261
MA0039.20.106
MA0040.10.91
MA0041.10.294
MA0042.10.798
MA0043.10.0542
MA0046.10.186
MA0047.20.186
MA0048.10.386
MA0050.11.42958e-7
MA0051.10.00144
MA0052.10.038
MA0055.10.976
MA0057.10.751
MA0058.10.0124
MA0059.10.207
MA0060.13.1392e-5
MA0061.10.201
MA0062.20.00104
MA0065.20.0182
MA0066.10.173
MA0067.10.345
MA0068.10.00387
MA0069.10.376
MA0070.10.499
MA0071.10.212
MA0072.10.947
MA0073.10.43
MA0074.10.1
MA0076.10.589
MA0077.10.332
MA0078.10.409
MA0079.20.327
MA0080.21.01114e-17
MA0081.11.66935e-4
MA0083.10.00703
MA0084.10.0928
MA0087.10.722
MA0088.10.0949
MA0090.10.0345
MA0091.10.17
MA0092.10.277
MA0093.10.123
MA0099.20.446
MA0100.10.892
MA0101.10.983
MA0102.20.0118
MA0103.10.86
MA0104.20.579
MA0105.10.0101
MA0106.10.968
MA0107.10.813
MA0108.23.00047e-7
MA0111.10.403
MA0112.21.43695e-4
MA0113.10.234
MA0114.10.0196
MA0115.10.592
MA0116.11.88741e-4
MA0117.10.861
MA0119.10.526
MA0122.10.571
MA0124.10.0563
MA0125.10.877
MA0131.10.397
MA0135.10.683
MA0136.13.62102e-14
MA0137.20.044
MA0138.20.873
MA0139.10.391
MA0140.10.859
MA0141.10.0229
MA0142.10.507
MA0143.10.467
MA0144.10.0218
MA0145.10.0811
MA0146.10.0361
MA0147.10.915
MA0148.10.972
MA0149.10.0692
MA0150.10.046
MA0152.10.548
MA0153.10.0449
MA0154.10.00475
MA0155.10.983
MA0156.19.32344e-8
MA0157.10.75
MA0159.10.0556
MA0160.10.0293
MA0162.10.552
MA0163.14.29282e-6
MA0164.10.437
MA0258.10.0049
MA0259.10.676



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: CNhs10861

Novel motifP-value
10.134
100.0209
1000.946
1010.254
1020.791
1030.198
1040.972
1050.486
1060.207
1070.453
1080.732
1090.0212
110.0613
1100.186
1110.0258
1120.094
1130.706
1140.03
1150.309
1160.736
1170.0233
1180.213
1190.123
120.513
1200.391
1210.568
1220.879
1230.271
1240.346
1250.363
1260.194
1270.19
1280.105
1290.639
130.036
1300.577
1310.884
1320.533
1330.842
1340.675
1350.0792
1360.749
1370.0173
1380.073
1390.0825
140.267
1400.417
1410.618
1420.183
1430.289
1440.46
1450.356
1460.834
1470.316
1480.0815
1490.516
150.178
1500.467
1510.782
1520.258
1530.886
1540.884
1550.182
1560.899
1570.773
1580.677
1590.229
160.232
1600.535
1610.658
1620.625
1630.71
1640.186
1650.268
1660.752
1670.558
1680.722
1690.0052
170.238
180.375
190.159
20.944
200.831
210.433
220.18
230.336
240.069
250.521
260.0847
270.197
280.641
290.226
30.0191
300.605
310.581
320.658
330.446
340.24
350.397
360.14
370.112
380.0635
390.772
40.995
400.147
410.286
420.414
430.0845
440.0923
450.71
460.193
470.265
480.196
490.205
50.289
500.792
510.565
520.366
530.226
540.417
550.0584
560.558
570.562
580.141
590.179
60.208
600.118
610.153
620.134
630.286
640.279
650.0823
660.981
670.338
680.946
690.582
70.202
700.0194
710.0582
720.189
730.0376
740.878
750.0168
760.216
770.224
780.0604
790.255
80.134
800.408
810.253
820.142
830.974
840.465
850.0604
860.0546
870.0929
880.244
890.152
90.412
900.0228
910.749
920.0962
930.859
940.0949
950.149
960.243
970.867
980.463
990.746



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: CNhs10861


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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