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FF:11384-118B7: 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 17:05, 29 March 2012


Name:Dendritic Cells - monocyte immature 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 stage65 years old adult
sexmale
age65
cell typedendritic cell, myeloid, immature
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberDC722
catalog number3H100-70-5
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-penis0.144
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0616
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.35
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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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: CNhs12000

Jaspar motifP-value
MA0002.20.0274
MA0003.10.0908
MA0004.10.486
MA0006.10.422
MA0007.10.261
MA0009.10.264
MA0014.10.255
MA0017.19.37662e-4
MA0018.23.51345e-4
MA0019.10.756
MA0024.16.24789e-4
MA0025.10.021
MA0027.10.686
MA0028.10.53
MA0029.10.805
MA0030.10.00815
MA0031.10.0574
MA0035.20.626
MA0038.10.00782
MA0039.20.167
MA0040.10.43
MA0041.10.114
MA0042.10.51
MA0043.10.00734
MA0046.10.268
MA0047.20.586
MA0048.10.869
MA0050.10.00616
MA0051.10.067
MA0052.10.302
MA0055.10.695
MA0057.10.257
MA0058.10.127
MA0059.10.239
MA0060.15.34439e-7
MA0061.10.171
MA0062.20.0498
MA0065.20.00325
MA0066.10.191
MA0067.10.686
MA0068.10.00196
MA0069.10.189
MA0070.10.466
MA0071.10.0557
MA0072.10.486
MA0073.10.486
MA0074.10.26
MA0076.10.338
MA0077.10.164
MA0078.10.324
MA0079.20.216
MA0080.26.06821e-16
MA0081.10.0031
MA0083.10.432
MA0084.10.0147
MA0087.10.311
MA0088.10.314
MA0090.10.0561
MA0091.10.194
MA0092.10.219
MA0093.10.441
MA0099.20.899
MA0100.10.809
MA0101.10.882
MA0102.20.684
MA0103.10.261
MA0104.21
MA0105.10.0419
MA0106.10.629
MA0107.11
MA0108.24.24775e-7
MA0111.10.323
MA0112.27.61366e-5
MA0113.10.108
MA0114.10.0167
MA0115.10.415
MA0116.14.77151e-4
MA0117.10.822
MA0119.10.688
MA0122.10.295
MA0124.10.495
MA0125.10.338
MA0131.10.463
MA0135.10.173
MA0136.12.96979e-12
MA0137.20.0198
MA0138.20.887
MA0139.10.348
MA0140.10.474
MA0141.10.00132
MA0142.10.967
MA0143.10.849
MA0144.10.0361
MA0145.10.0686
MA0146.10.0126
MA0147.10.942
MA0148.10.289
MA0149.10.177
MA0150.10.126
MA0152.10.106
MA0153.10.0299
MA0154.10.00558
MA0155.10.659
MA0156.17.63104e-5
MA0157.10.385
MA0159.10.012
MA0160.10.00458
MA0162.10.46
MA0163.11.20757e-4
MA0164.10.903
MA0258.10.0018
MA0259.10.503



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: CNhs12000

Novel motifP-value
10.0319
100.035
1000.76
1010.162
1020.541
1030.104
1040.244
1050.649
1060.00737
1070.176
1080.849
1090.0178
110.0448
1100.166
1110.008
1120.0202
1130.609
1140.00333
1150.67
1160.354
1170.0426
1180.348
1190.0193
120.403
1200.189
1210.84
1220.397
1230.225
1240.545
1250.337
1260.393
1270.0939
1280.0258
1290.431
130.0936
1300.484
1310.703
1320.875
1330.885
1340.669
1350.0126
1360.195
1370.114
1380.336
1390.0412
140.273
1400.123
1410.982
1420.464
1430.108
1440.432
1450.395
1460.921
1470.35
1480.0097
1490.19
150.211
1500.482
1510.546
1520.0432
1530.524
1540.821
1550.189
1560.766
1570.727
1580.892
1590.481
160.203
1600.366
1610.254
1620.87
1630.408
1640.06
1650.216
1660.555
1670.667
1680.911
1690.00329
170.145
180.287
190.131
20.798
200.792
210.163
220.168
230.272
240.0261
250.73
260.0747
270.181
280.628
290.293
30.0215
300.92
310.589
320.73
330.324
340.418
350.677
360.216
370.0687
380.18
390.673
40.89
400.128
410.597
420.483
430.0676
442.34117e-4
450.819
460.127
470.151
480.185
490.179
50.596
500.85
510.49
520.187
530.515
540.257
550.0682
560.701
570.431
580.205
590.0787
60.788
600.0819
610.277
620.143
630.322
640.261
650.0859
660.693
670.22
680.889
690.332
70.288
700.0474
710.0602
720.257
730.0175
740.486
750.0501
760.387
770.106
780.0226
790.109
80.0602
800.57
810.175
820.0923
830.966
840.378
850.0198
860.0403
870.0307
880.216
890.0646
90.349
900.0837
910.72
920.272
930.798
940.0835
950.135
960.153
970.917
980.124
990.752



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: CNhs12000


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)
0000451 (dendritic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000837 (hematopoietic multipotent progenitor cell)
0000840 (immature conventional dendritic cell)
0000988 (hematopoietic cell)
0000990 (conventional dendritic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0001019 (CD115-positive monocyte OR common dendritic progenitor)
0001029 (common dendritic progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
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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