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FF:12131-128D7: 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 17:21, 29 March 2012


Name:granulocyte macrophage progenitor, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typegranulocyte macrophage progenitor
cell lineNA
companyNA
collaborationLennartsson
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA
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-0.195
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs12519

Jaspar motifP-value
MA0002.20.111
MA0003.10.956
MA0004.10.209
MA0006.10.333
MA0007.10.606
MA0009.10.749
MA0014.10.975
MA0017.10.901
MA0018.24.97156e-5
MA0019.10.467
MA0024.11.84111e-6
MA0025.12.28722e-4
MA0027.10.107
MA0028.10.331
MA0029.10.369
MA0030.10.0731
MA0031.10.236
MA0035.20.0752
MA0038.10.88
MA0039.20.523
MA0040.10.0654
MA0041.10.0858
MA0042.10.111
MA0043.13.89389e-6
MA0046.10.0104
MA0047.20.0915
MA0048.10.883
MA0050.10.138
MA0051.10.101
MA0052.10.831
MA0055.10.592
MA0057.10.661
MA0058.10.254
MA0059.10.71
MA0060.11.00921e-4
MA0061.10.136
MA0062.23.68118e-6
MA0065.20.0852
MA0066.10.0141
MA0067.10.0032
MA0068.10.118
MA0069.10.115
MA0070.10.0577
MA0071.10.891
MA0072.10.781
MA0073.10.989
MA0074.10.313
MA0076.10.0284
MA0077.10.837
MA0078.10.673
MA0079.20.0308
MA0080.24.37997e-11
MA0081.14.73384e-4
MA0083.10.0459
MA0084.10.838
MA0087.10.968
MA0088.10.324
MA0090.11.76956e-4
MA0091.10.832
MA0092.10.112
MA0093.10.162
MA0099.20.21
MA0100.11.33188e-4
MA0101.10.918
MA0102.27.49852e-4
MA0103.10.31
MA0104.20.207
MA0105.15.40494e-5
MA0106.10.0806
MA0107.10.478
MA0108.22.50496e-5
MA0111.10.282
MA0112.29.40551e-5
MA0113.10.655
MA0114.10.376
MA0115.10.414
MA0116.10.0109
MA0117.10.418
MA0119.10.0282
MA0122.10.137
MA0124.10.0965
MA0125.10.868
MA0131.10.279
MA0135.10.0277
MA0136.11.90476e-9
MA0137.20.847
MA0138.20.175
MA0139.10.0984
MA0140.10.411
MA0141.10.118
MA0142.10.83
MA0143.10.901
MA0144.10.931
MA0145.10.0723
MA0146.10.571
MA0147.10.361
MA0148.10.712
MA0149.10.944
MA0150.10.287
MA0152.10.0693
MA0153.10.571
MA0154.10.0714
MA0155.10.861
MA0156.14.87411e-7
MA0157.10.824
MA0159.10.0202
MA0160.10.564
MA0162.10.133
MA0163.10.0127
MA0164.10.982
MA0258.10.00602
MA0259.10.594



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: CNhs12519

Novel motifP-value
10.0246
100.552
1000.194
1010.797
1020.831
1030.797
1040.941
1050.981
1060.551
1070.246
1080.283
1090.359
110.111
1100.0773
1110.194
1120.644
1130.508
1140.172
1150.279
1160.134
1170.588
1180.687
1190.0508
120.745
1200.308
1210.954
1220.617
1230.0652
1240.341
1250.178
1260.415
1270.21
1280.939
1290.46
130.319
1300.542
1310.0654
1320.222
1330.636
1340.245
1350.303
1360.319
1370.0137
1380.605
1390.43
140.983
1400.929
1410.738
1420.724
1430.951
1440.474
1450.145
1460.767
1470.146
1480.0912
1490.252
150.857
1500.74
1510.618
1520.765
1530.184
1540.452
1550.0172
1560.567
1570.3
1580.251
1590.664
160.0359
1600.0865
1610.821
1620.221
1630.862
1640.616
1650.44
1660.815
1670.43
1680.395
1690.00503
170.213
180.357
190.0482
20.762
200.984
210.169
220.891
230.173
240.49
250.923
260.862
270.876
280.812
290.913
30.0727
300.963
310.523
321.95615e-4
330.354
340.615
350.33
360.345
370.212
380.454
390.329
40.695
400.234
410.574
420.411
430.126
440.0163
450.761
460.0955
470.144
480.214
490.356
50.457
500.832
510.649
520.963
530.878
540.806
550.533
560.304
570.155
580.573
590.284
60.288
600.718
610.689
620.449
630.1
640.192
650.0957
660.547
670.6
680.581
690.167
70.838
700.0176
710.0898
720.898
730.451
740.696
750.472
760.491
770.062
780.172
790.049
80.049
800.265
810.274
820.0469
830.524
840.979
850.0885
860.742
870.122
880.12
890.0135
90.723
900.658
910.344
920.0129
930.878
940.397
950.925
960.342
970.892
980.395
990.0305



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: CNhs12519


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)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000763 (myeloid cell)
0000837 (hematopoietic multipotent progenitor cell)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002032 (hematopoietic oligopotent progenitor 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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