FF:10776-110G2: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |DRA_sample_Accession=CAGE@SAMD00021196 | ||
| | |accession_numbers=CAGE;DRX022764;DRR025103;DRZ003528;DRZ004411;DRZ008269;DRZ009152 | ||
| | |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002046,UBERON:0004119,UBERON:0010314,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0002530,UBERON:0010317,UBERON:0000949 | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
| | |ancestors_in_disease_facet=DOID:4,DOID:0050686,DOID:162,DOID:14566,DOID:170,DOID:1781,DOID:3963 | ||
|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000210,FF:0000101,FF:0000001,FF:0101610 | |||
|comment= | |||
|created_by= | |||
|creation_date= | |||
|data_phase=2 | |||
|datafreeze_phase=2 | |||
|def= | |||
|f5samples= | |||
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0007123,UBERON:0010316 | |||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
Line 66: | Line 40: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |||
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/thyroid%2520carcinoma%2520cell%2520line%253aKHM-5M.CNhs14140.10776-110G2.hg19.nobarcode.bam | |||
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/thyroid%2520carcinoma%2520cell%2520line%253aKHM-5M.CNhs14140.10776-110G2.hg19.ctss.bed.gz | |||
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/thyroid%2520carcinoma%2520cell%2520line%253aKHM-5M.CNhs14140.10776-110G2.hg19.nobarcode.rdna.fa.gz | |||
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/thyroid%2520carcinoma%2520cell%2520line%253aKHM-5M.CNhs14140.10776-110G2.hg38.nobarcode.bam | |||
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/thyroid%2520carcinoma%2520cell%2520line%253aKHM-5M.CNhs14140.10776-110G2.hg38.nobarcode.ctss.bed.gz | |||
|id=FF:10776-110G2 | |||
|is_a=DOID:3963;;EFO:0002091;;FF:0000210;;FF:0101610 | |||
|is_obsolete= | |||
|library_id=CNhs14140 | |||
|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;10776 | |||
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10776 | |||
|name=thyroid carcinoma cell line:KHM-5M | |||
|namespace=FANTOM5 | |||
|part_of= | |||
|profile_cagescan= | |||
|profile_hcage=CNhs14140,LSID1159,release016,COMPLETED | |||
|profile_rnaseq= | |||
|profile_srnaseq= | |||
|rna_box=110 | |||
|rna_catalog_number= | |||
|rna_concentration=2.42187 | |||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |||
|rna_lot_number= | |||
|rna_od260/230=2.12 | |||
|rna_od260/280=2.04 | |||
|rna_position=G2 | |||
|rna_rin= | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=110G2 | |||
|rna_weight_ug=65.39049 | |||
|sample_age=65 | |||
|sample_category=cell lines | |||
|sample_cell_catalog=jcrb0148 | |||
|sample_cell_line=KHM-5M | |||
|sample_cell_lot= | |||
|sample_cell_type=unclassifiable | |||
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest) | |||
|sample_company=JAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank | |||
|sample_description= | |||
|sample_dev_stage= | |||
|sample_disease=thyroid carcinoma | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity=J | |||
|sample_experimental_condition= | |||
|sample_id=10776 | |||
|sample_note= | |||
|sample_sex=male | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue=thyroid | |||
|top_motifs= | |top_motifs= | ||
|xref= | |||
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10776-110G2;search_select_hide=table117:FF:10776-110G2 | |||
}} | }} |
Latest revision as of 15:03, 3 June 2020
Name: | thyroid carcinoma cell line:KHM-5M |
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Species: | Human (Homo sapiens) |
Library ID: | CNhs14140 |
Sample type: | cell lines |
Genomic View: | UCSC |
CAGEd-oPOSSUM: | link |
ZENBU report : | link |
ExpandAdditional information |
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ExpandCAGE Accession numbers |
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ExpandDownload raw sequence, BAM & CTSS |
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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: CNhs14140This 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: CNhs14140This 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: CNhs14140
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
DOID:3963 thyroid carcinoma
EFO:0002091 biological replicate
FF:0000210 human sample
FF:0101610 thyroid cancer cell line sample
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
DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
170 (endocrine gland cancer)
1781 (thyroid cancer)
3963 (thyroid carcinoma)
UBERON: Anatomy
0000468 (multi-cellular organism)
0002046 (thyroid gland)
0004119 (endoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0000949 (endocrine system)
FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0101610 (thyroid cancer cell line 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
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0007123 (pharyngeal pouch 2)
UBERON:0010316 (germ layer / neural crest)