Personal tools

FF:10272-104E2: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005520
|DRA_sample_Accession=CAGE@SAMD00005520
|accession_numbers=CAGE;DRX008650;DRR009522;DRZ000947;DRZ002332
|accession_numbers=CAGE;DRX008650;DRR009522;DRZ000947;DRZ002332;DRZ012297;DRZ013682
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001134,UBERON:0006322,UBERON:0004277,UBERON:0000970,UBERON:0000019,UBERON:0000033,UBERON:0000479,UBERON:0004121,UBERON:0010314,UBERON:0000047,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0001444,UBERON:0000477,UBERON:0000467,UBERON:0010313,UBERON:0001062,UBERON:0000480,UBERON:0000020,UBERON:0002036,UBERON:0002385,UBERON:0002376,UBERON:0005090,UBERON:0001630,UBERON:0001032,UBERON:0010959,UBERON:0003899,UBERON:0010317,UBERON:0001577,UBERON:0008229,UBERON:0004461,UBERON:0006533,UBERON:0001601,UBERON:0006531,UBERON:0001015,UBERON:0004088,UBERON:0000153,UBERON:0007811,UBERON:0002204,UBERON:0002104,UBERON:0000383,UBERON:0004456,UBERON:0001456,UBERON:0004473,UBERON:0003269
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001134,UBERON:0006322,UBERON:0004277,UBERON:0000970,UBERON:0000019,UBERON:0000033,UBERON:0000479,UBERON:0004121,UBERON:0010314,UBERON:0000047,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0001444,UBERON:0000477,UBERON:0000467,UBERON:0010313,UBERON:0001062,UBERON:0000480,UBERON:0000020,UBERON:0002036,UBERON:0002385,UBERON:0002376,UBERON:0005090,UBERON:0001630,UBERON:0001032,UBERON:0010959,UBERON:0003899,UBERON:0010317,UBERON:0001577,UBERON:0008229,UBERON:0004461,UBERON:0006533,UBERON:0001601,UBERON:0006531,UBERON:0001015,UBERON:0004088,UBERON:0000153,UBERON:0007811,UBERON:0002204,UBERON:0002104,UBERON:0000383,UBERON:0004456,UBERON:0001456,UBERON:0004473,UBERON:0003269
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
Line 9: Line 9:
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=1
|data_phase=2
|datafreeze_phase=1
|datafreeze_phase=2
|def=
|def=
|fantom_cat=http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0001601
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0006603,UBERON:0003104,UBERON:0005062,UBERON:0007284,UBERON:0009920,UBERON:0003063,UBERON:0003099,UBERON:0010316
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0006603,UBERON:0003104,UBERON:0005062,UBERON:0007284,UBERON:0009920,UBERON:0003063,UBERON:0003099,UBERON:0010316
|fonse_cell_line=
|fonse_cell_line=
Line 40: Line 41:
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/eye%2520-%2520muscle%2520inferior%2520rectus%252c%2520donor1.CNhs13444.10272-104E2.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/eye%2520-%2520muscle%2520inferior%2520rectus%252c%2520donor1.CNhs13444.10272-104E2.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/eye%2520-%2520muscle%2520inferior%2520rectus%252c%2520donor1.CNhs13444.10272-104E2.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/eye%2520-%2520muscle%2520inferior%2520rectus%252c%2520donor1.CNhs13444.10272-104E2.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/eye%2520-%2520muscle%2520inferior%2520rectus%252c%2520donor1.CNhs13444.10272-104E2.hg38.nobarcode.ctss.bed.gz
|id=FF:10272-104E2
|id=FF:10272-104E2
|is_a=EFO:0002091;;FF:0011153
|is_a=EFO:0002091;;FF:0011153
|is_obsolete=
|is_obsolete=
|library_id=CNhs13444
|library_id=CNhs13444
|library_id_phase_based=1:CNhs13444
|library_id_phase_based=2:CNhs13444
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10272
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10272
|name=eye - muscle inferior rectus, donor1
|name=eye - muscle inferior rectus, donor1
|namespace=
|namespace=
Line 50: Line 60:
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs13444,LSID1024,release012,COMPLETED
|profile_hcage=CNhs13444,LSID1024,release012,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|rna_box=104
|rna_box=104
Line 62: Line 72:
|rna_rin=3.6
|rna_rin=3.6
|rna_sample_type=total RNA
|rna_sample_type=total RNA
|rna_tube_id=104E2
|rna_tube_id=1.04E+04
|rna_weight_ug=9.139
|rna_weight_ug=9.139
|sample_age=
|sample_age=
Line 86: Line 96:
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10272-104E2;search_select_hide=table117:FF:10272-104E2
}}
}}

Latest revision as of 13:57, 3 June 2020

Name:eye - muscle inferior rectus, donor1
Species:Human (Homo sapiens)
Library ID:CNhs13444
Sample type:tissues
Genomic View: UCSC
FANTOM CAT:1
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueeye - muscle inferior rectus
dev stageNA
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationAlessandro Bonetti
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1-Ey6
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005520
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13444 CAGE DRX008650 DRR009522
Accession ID Hg19

Library idBAMCTSS
CNhs13444 DRZ000947 DRZ002332
Accession ID Hg38

Library idBAMCTSS
CNhs13444 DRZ012297 DRZ013682
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: CNhs13444This 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: CNhs13444This 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: CNhs13444


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0001134 (skeletal muscle tissue)
0006322 (inferior rectus extraocular muscle)
0004277 (eye muscle)
0000970 (eye)
0000019 (camera-type eye)
0000033 (head)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0000047 (simple eye)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0010313 (neural crest-derived structure)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0002036 (striated muscle tissue)
0002385 (muscle tissue)
0002376 (cranial muscle)
0005090 (muscle structure)
0001630 (muscle organ)
0001032 (sensory system)
0010959 (craniocervical muscle)
0003899 (skeletal muscle of head)
0010317 (germ layer / neural crest derived structure)
0001577 (muscle of face)
0008229 (craniocervical region musculature)
0004461 (musculature of head)
0006533 (rectus extraocular muscle)
0001601 (extra-ocular muscle)
0006531 (oculomotor muscle)
0001015 (musculature)
0004088 (ocular region)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002204 (musculoskeletal system)
0002104 (visual system)
0000383 (musculature of body)
0004456 (entire sense organ system)
0001456 (face)
0004473 (musculature of face)
0003269 (skeletal muscle tissue of eye)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011153 (human eye - muscle inferior rectus 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:0006601 (presumptive ectoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0003104 (mesenchyme)
UBERON:0005062 (neural fold)
UBERON:0007284 (presumptive neural plate)
UBERON:0009920 (optic neural crest)
UBERON:0003063 (prechordal plate)
UBERON:0003099 (cranial neural crest)
UBERON:0010316 (germ layer / neural crest)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:10272-104E2&oldid=4575966"