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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00022299
|accession_numbers=CAGE;DRX022772;DRR025111;DRZ003536;DRZ004419;DRZ008277;DRZ009160
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0000763,CL:0002371,CL:0000766,CL:0000219,CL:0000738,CL:0002087,CL:0000255,CL:0000576
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0000763,CL:0002371,CL:0000766,CL:0000219,CL:0000738,CL:0002087,CL:0000255,CL:0000576
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|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|ffid_belonging_in_development=CL:0000049,CL:0000134
|ffid_belonging_in_development=CL:0000049,CL:0000134
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|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.fractionation.hCAGE/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M5%2529%2520cell%2520line%253aTHP-1%2520%2528cytoplasmic%2520fraction%2529.CNhs14556.14298-155B5.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.fractionation.hCAGE/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M5%2529%2520cell%2520line%253aTHP-1%2520%2528cytoplasmic%2520fraction%2529.CNhs14556.14298-155B5.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.fractionation.hCAGE/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M5%2529%2520cell%2520line%253aTHP-1%2520%2528cytoplasmic%2520fraction%2529.CNhs14556.14298-155B5.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.fractionation.hCAGE/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M5%2529%2520cell%2520line%253aTHP-1%2520%2528cytoplasmic%2520fraction%2529.CNhs14556.14298-155B5.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.fractionation.hCAGE/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M5%2529%2520cell%2520line%253aTHP-1%2520%2528cytoplasmic%2520fraction%2529.CNhs14556.14298-155B5.hg38.nobarcode.ctss.bed.gz
|id=FF:14298-155B5
|id=FF:14298-155B5
|is_a=EFO:0002091;;FF:0000210;;FF:0000661
|is_a=EFO:0002091;;FF:0000210;;FF:0000661
|is_obsolete=
|is_obsolete=
|library_id=CNhs14556
|library_id_phase_based=2:
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;14298
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;14298
|name=acute myeloid leukemia (FAB M5) cell line:THP-1 (cytoplasmic fraction)
|name=acute myeloid leukemia (FAB M5) cell line:THP-1 (cytoplasmic fraction)
|namespace=FANTOM5
|namespace=FANTOM5
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|rna_weight_ug=90.71
|rna_weight_ug=90.71
|sample_age=
|sample_age=
|sample_category=fractionations and perturbations
|sample_cell_catalog=
|sample_cell_catalog=
|sample_cell_line=THP-1
|sample_cell_line=THP-1
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|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:14298-155B5;search_select_hide=table117:FF:14298-155B5
}}
}}

Latest revision as of 19:05, 4 June 2020


Name:acute myeloid leukemia (FAB M5) cell line:THP-1 (cytoplasmic fraction)
Species:Human (Homo sapiens)
Library ID:CNhs14556
Sample type:fractionations and perturbations
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainUNDEFINED_STRAIN
tissueblood
dev stage1 year old child
sexmale
ageNA
cell typemonoblast
cell lineTHP-1
companyNA
collaborationUNDEFINED_COLLABORATION
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00022299
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14556 CAGE DRX022772 DRR025111
Accession ID Hg19

Library idBAMCTSS
CNhs14556 DRZ003536 DRZ004419
Accession ID Hg38

Library idBAMCTSS
CNhs14556 DRZ008277 DRZ009160
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload





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>dataNo results for this sample

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: CNhs14556This sample isn't target for the analysis

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: CNhs14556This sample isn't target for the analysis

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: CNhs14556


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000766 (myeloid leukocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0000255 (eukaryotic cell)
0000576 (monocyte)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
2531 (hematologic cancer)
14566 (disease of cellular proliferation)
0060083 (immune system cancer)
1240 (leukemia)
8692 (myeloid leukemia)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100737 (leukemia cell line sample)
0000408 (cellular fractionation sample)
0000350 (experimentally modified sample)
0000405 (cytoplasmic fraction sample)
0101370 (THP-1 cell sample)
0101035 (hematopoietic cell line sample)
0102332 (monocytic leukemia cell line sample)
0100740 (myeloid leukemia cell line sample)
0000661 (acute myeloid leukemia (FAB M5) cell line:THP-1 cytoplasmic fraction sample)

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
CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)

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