RefEx

2020/03/31

Web Site: https://refex.dbcls.jp/index.php?lang=en
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/refex/

The database of gene expression data in each tissue.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Data Relationship Matrix
  3. Gene Expression Data
  4. Tissue Specific Gene Expression Data
  5. ID Relation Table
  6. Tissue 10/40 Table
  7. Sample Annotations
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "RefEx" data.
File README_e.html (English)
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2.2 Data Relationship Matrix

Data name Data Relationship Matrix
Description of data contents

A table of the relationship among different type of data.
File refex_data_relationship_matrix.zip (1 KB)

Data items are the following:
Data itemDescription
Species Species of object
Experimental Method Experimantal method of collecting expression data.
Kind of ID Kind of ID
Gene Expression (classificated in 10 organs) Gene expression data classified in 10 organs.
Gene Expression (classificated in 10 organs) DOI DOI of gene expression data classificated in 10 organs.
Gene Expression (classificated in 40 organs) Gene expression data classified in 40 organs.
Gene Expression (classificated in 40 organs) DOI DOI of gene expression data classificated in 40 organs.
Gene Expression (by FANTOM5 CAGE) CAGE data collected by FANTOM5.
Gene Expression (by FANTOM5 CAGE) DOI DOI of CAGE data collected by FANTOM5.
Sample Classification Table Classification table of each tissue.
Sample Classification Table DOI DOI of classification table of each tissue.
Sample Annotation Information of sample annotation
Sample Annotation DOI DOI of information of sample annotation.
Tissue Specificity (calculated by ROKU) Tissue specificity calculated by ROKU method.
Tissue Specificity (calculated by ROKU) DOI DOI of tissue specificity calculated by ROKU method.
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2.3 Gene Expression Data

Data name Gene Expression Data
Description of data contents

Gene expression data collected by EST, GeneChip, CAGE, or RNA-seq Each data is named "RefEx_expression_[experimental method][the number of tissue classes]_[species]" in general.
e.g. RefEx_expression_EST10_human

Nevertheless, some data collected by CAGE are named "RefEx_expression_CAGE_all_[species]".
e.g. RefEx_expression_CAGE_all_human
File refex_expression01_cage10_human_prjdb1099.zip (908 KB)
refex_expression02_cage40_human_prjdb1099.zip (2.5 MB)
refex_expression03_cage_all_human_prjdb1099.zip (40.5 MB)
refex_expression04_cage_all_mouse_prjdb1100.zip (21.2 MB)
refex_expression05_est10_human.zip (597 KB)
refex_expression06_est10_mouse.zip (592 KB)
refex_expression07_est10_rat.zip (421 KB)
refex_expression08_est40_human.zip (1.2 MB)
refex_expression09_est40_mouse.zip (1.1 MB)
refex_expression10_est40_rat.zip (550 KB)
refex_expression11_genechip10_human_gse7307.zip (1.1 MB)
refex_expression12_genechip10_mouse_gse10246.zip (898 KB)
refex_expression13_genechip10_rat_gse952.zip (143 KB)
refex_expression14_genechip40_human_gse7307.zip (10.6 MB)
refex_expression15_genechip40_mouse_gse10246.zip (2.8 MB)
refex_expression16_genechip40_rat_gse952.zip (326 KB)
refex_expression17_rnaseq10_human_prjeb2445.zip (1.9 MB)
refex_expression18_rnaseq10_mouse_prjna30467.zip (307 KB)
refex_expression19_rnaseq40_human_prjeb2445.zip (3.2 MB)
refex_expression20_rnaseq40_mouse_prjna30467.zip (344 KB)
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2.4 Tissue Specific Gene Expression Data

Data name Tissue Specific Gene Expression Data
Description of data contents

Data of tissue specific gene expression calculated by ROKU method.
File refex_tissue_specific01_genechip_human_gse7307.zip (560 KB)
refex_tissue_specific02_genechip_mouse_gse10246.zip (485 KB)
refex_tissue_specific03_genechip_rat_gse952.zip (97 KB)
refex_tissue_specific04_rnaseq_human_prjeb2445.zip (462 KB)

Data items are the following:
Data itemDescription
ID In GeneChip data and RNA-Seq data, Probe set ID by Affymetrix and NCBI RefSeq ID respectively.
score Entropy score. When this score is smaller, specificity of the gene is higher.
v[tissue ID in RefEx]_[name of tissue] For each tissue, 1: specific high expression, -1: specific low expression, 0: others
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2.5 ID Relation Table

Data name ID Relation Table
Description of data contents

Relation table of Gene IDs.
File refex_id_relation_human.zip (388 KB)
refex_id_relation_mouse.zip (406 KB)
refex_id_relation_rat.zip (167 KB)

Data items are the following:
Data itemDescription
NCBI_GeneID NCBI Entrez Gene ID
NCBI_UnigeneID NCBI Unigene ID
NCBI_RefSeqID NCBI RefSeq ID
Affymetrix_probesetID Affymetrix probeset ID
organism Organism
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2.6 Tissue 10/40 Table

Data name Tissue 10/40 Table
Description of data contents

Tissue classification in RefEx.
As column names of sample ID, "GSM_#" are used in GeneChip data, while "SINGLE" and "PAIRED" in RNA-Seq data.
File refex_10_40_classifications01_genechip_human_gse7307.zip (3 KB)
refex_10_40_classifications02_genechip_mouse_gse10246.zip (1 KB)
refex_10_40_classifications03_genechip_rat_gse952.zip (1 KB)
refex_10_40_classifications04_rnaseq_human_prjeb2445.zip (1 KB)
refex_10_40_classifications05_rnaseq_mouse_prjna30467.zip (1 KB)

Data items are the following:
Data itemDescription
Description (RefEx refined) Tissue name
10 groups ID of each tissue classified in 10 organs.
40 groups ID of each tissue classified in 40 organs.
GSM_# IDs of all samples used in experiments of each tissue.
SINGLE Data on Single-End RNA-Seq
PAIRED Data on Pair-End RNA-Seq
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2.7 Sample Annotations

Data name Sample Annotations
Description of data contents

Sample annotations provided by each project.
Columns are different in CAGE data and GeneChip data.
File refex_sample_ann01_cage_human_prjdb1099 (27 KB)
refex_sample_ann02_cage_mouse_prjdb1100 (11 KB)
refex_sample_ann03_genechip_mouse_gse10246 (3 KB)
refex_sample_ann04_genechip_rat_gse952 (2 KB)

Data items are the following:
Data itemDescription
CAGE
FANTOM5 Original Order Order defined in FANTOM5
Alphabetical Uniq Order by developmental, primary cells Alphabetical order
RefEx Tissue Class10 ID of each tissue classified in 10 organs.
RefEx Tissue Class40 ID of each tissue classified in 40 organs.
Cell Class Class of cell based on its property.
Tissue Class Class of tissue based on its property.
Description (RefEx refined) Additional information on samples provided by RefEx.
FANTOM5 URL URL for information on samples provided by FANTOM5.
Description (FANTOM5) Additional information on samples provided by FANTOM5.
GeneChip
Accession GEO accession of sample
Title Sample name
Sample Type Type of sample
Taxonomy Organism
Channels The number of kind of fluorescent pigments in Microarray.
Platform GEO accession of experimental platform
Series GEO accession of series the sample belongs in.
Supplementary Types Formats of available raw data file
Supplementary Links URL for raw data file
SRA Accession SRA accession
Contact Contact about data
Release Date Release date of data
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3. License

Last updated : 2020/03/31

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

Creative Commons License

The license for this database is specified in the Creative Commons Attribution 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "RefExcDBCLS licensed under CC Attribution 4.0 International".

The summary of the Creative Commons Attribution 4.0 International is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other adapted materials based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
  2. You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

https://dbcls.rois.ac.jp/contact

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

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4. Update History

DateUpdate contents
2020/03/31 RefEx English archive site is opened.
2014/04/01 RefEx (https://refex.dbcls.jp/index.php?lang=en) is opened.
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5. Literature

Ono H, Ogasawara O, Okubo K, Bono H
RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes
Scientific data/Aug 2017/vol. 4 170105
PMID: 28850115

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6. Contact address

When you have any question about "RefEx", contact the following:

https://dbcls.rois.ac.jp/contact

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