ChIP-Atlas
2021/10/14Web Site: https://chip-atlas.org/
The database of the result of analysis processed from the entire ChIP-Seq data archived in Sequence Read Archive.
README Content
1. Database Component
2. Data Description
2.1 README
| Data name | README |
|---|---|
| Description of data contents | HTML file to describe "ChIP-Atlas" data. |
| File | README_e.html (English) |
2.2 Experiment list
| Data name | Experiment list |
|---|---|
| Description of data contents | A list of metadata of the reanalysed ChIP-Seq data archived in Sequence Read Archive (SRA), grouped by SRA Experiment ID, providing the information of reference genome data, antigen, or cell type. See details here: https://github.com/inutano/chip-atlas/wiki#downloads_doc |
| File | chip_atlas_experiment_list.zip (29 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| Experimental ID | Experimental ID (SRX, ERX, DRX) |
| Genome assembly | Genome assembly |
| Antigen class | Antigen class |
| Antigen | Antigen |
| Cell type class | Cell type class |
| Cell type | Cell type |
| Cell type description | Cell type description |
| Processing logs | Processing logs (# of reads, % mapped, % duplicates, # of peaks [q < 1E-05]) |
| Title | Title submitted by authors |
| Meta data | Meta data submitted by authors |
| BigWig | Link to a BigWig-formatted coverage score binary file. |
| Peak-call (BED) (q < 1E-05) | Link to a BED4-formatted peak-call data file with the q-value threshold 1E-05. |
| Peak-call (BED) (q < 1E-10) | Link to a BED4-formatted peak-call data file with the q-value threshold 1E-10. |
| Peak-call (BED) (q < 1E-20) | Link to a BED4-formatted peak-call data file with the q-value threshold 1E-20. |
| Peak-call (BigBed) (q < 1E-05) | Link to a BigBed-formatted peak-call data file binarized from the corresponding BED4 file (q < 1E-05). |
| Peak-call (BigBed) (q < 1E-10) | Link to a BigBed-formatted peak-call data file binarized from the corresponding BED4 file (q < 1E-10). |
| Peak-call (BigBed) (q < 1E-20) | Link to a BigBed-formatted peak-call data file binarized from the corresponding BED4 file (q < 1E-20). |
2.3 File list
| Data name | File list |
|---|---|
| Description of data contents | A list of merged bed file and its metadata, including reference genome data, antigen, cell type, and identifier of merged experiments. See details here: https://github.com/inutano/chip-atlas/wiki#downloads_doc |
| File | chip_atlas_file_list.zip (20 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| File name | File name |
| Genome assembly | Genome assembly |
| Antigen class | Antigen class |
| Antigen | Antigen |
| Cell type class | Cell type class |
| Cell type | Cell type |
| Threshold | Threshold |
| Experimental IDs included | Experimental IDs included |
| Peak-call (BED) | Link to a BED9 + GFF3 format file concatenated and converted from the BED4-formatted peak-call data files of the experiments in the "Experimental IDs included". |
2.4 Analysis list
| Data name | Analysis list |
|---|---|
| Description of data contents | A list of metadata to generate file paths of analysis provided on ChIP-Atlas, target gene analysis and colocalization analysis. See details here: https://github.com/inutano/chip-atlas/wiki#downloads_doc |
| File | chip_atlas_analysis_list.zip (126 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Antigen | Antigen |
| Cell type class in Colocalization | Cell type class in Colocalization (comma separated) |
| Recorded (+) or not (-) in Target Genes | Target gene analysis performed or not (+/-) |
| Genome assembly | Genome assembly |
| Target Genes (TSS ±1k) | Link to a TSV (Tab-Separeted Values) file that describes the genes bound by the given antigen in the range of ± 1 kb of each TSS (transcription start site). |
| Target Genes (TSS ±5k) | Link to a TSV (Tab-Separeted Values) file that describes the genes bound by the given antigen in the range of ± 5 kb of each TSS (transcription start site). |
| Target Genes (TSS ±10k) | Link to a TSV (Tab-Separeted Values) file that describes the genes bound by the given antigen in the range of ± 10 kb of each TSS (transcription start site). |
| Colocalization (TSV) | Link to a TSV (Tab-Separeted Values) file that describes the protein colocalization with the given antigen in the given cell type class. |
| Colocalization (GML) | Link to a GML (Graph Modelling Language) file that describes the protein colocalization in the given cell type class. |
2.5 Antigen list
| Data name | Antigen list |
|---|---|
| Description of data contents | A list of all antigen names of data provided on ChIP-Atlas. See details here: https://github.com/inutano/chip-atlas/wiki#downloads_doc |
| File | chip_atlas_antigen_list.zip (1.1 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| Genome assembly | Genome assembly |
| Antigen class | Antigen class |
| Antigen | Antigen |
| Number of experiments | Number of experiments |
| Experimental IDs included | Experimental IDs included |
2.6 Cell type list
| Data name | Cell type list |
|---|---|
| Description of data contents | A list of all cell type names of data provided on ChIP-Atlas. See details here: https://github.com/inutano/chip-atlas/wiki#downloads_doc |
| File | chip_atlas_celltype_list.zip (1.1 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| Genome assembly | Genome assembly |
| Cell type class | Cell type class |
| Cell type | Cell type |
| Number of experiments | Number of experiments |
| Experimental IDs included | Experimental IDs included |
2.7 Data directory
| Data name | Data directory |
|---|---|
| Description of data contents | All ChIP-Seq data analyzed on ChIP-Atlas. BigWig, Bed, BigBed format files are provided for each individual Experiment. Bed files are provided for data assembled by antigens and cell types. Analysis data from target genes analysis and colocalization analysis are provided in tab separated values (tsv). See details here: https://github.com/inutano/chip-atlas/wiki#peak_browser_doc * The dataset of past version can not be downloaded. |
| File | hg19 (30 TB)
hg38 (30 TB) mm9 (24 TB) mm10 (24 TB) ce10 (291 GB) ce11 (292 GB) dm3 (874 GB) dm6 (827 GB) saccer3 (213 GB) rn6 (839 GB) |
3. License
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.
The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "ChIP-Atlas © Shinya Oki (Kyoto University) licensed under CC Attribution-Share Alike 4.0 International".
The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- 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:
- 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.
- You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
- 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.
Shinya Oki
Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine
Medical Innovation Center, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
E-mail: oki[dot]shinya[dot]3w[at]kyoto-u[dot]ac[dot]jp
About Providing Links to This Database
You can freely provide links to all contents in this database. But, contents might be changed without notice.
4. Update History
| Date | Update contents |
|---|---|
| 2021/09/21 | Archive version V19 Released. These data are updated. |
| Date | Update contents |
| 2020/09/04 | Archive version V19 Released. These data are updated. |
| 2020/05/14 | Archive version V18 Released. These data are updated. |
| 2020/01/10 | Archive version V17 Released. These data are updated. |
| 2019/11/08 | Archive version V16 Released. These data are updated. |
| 2019/04/05 | Archive version V15 Released. These data are updated. |
| 2018/10/12 | Archive version V14 Released. These data are updated. |
| 2018/08/02 | Archive version V13 Released. These data are updated. |
| 2018/05/25 | Archive version V12 Released. These data are updated. |
| 2018/02/22 | Archive version V11 Released. These data are updated. |
| 2018/01/15 | Archive version V10 Released. New organism "Rattus norvegicus" is added and these data are updated. |
| 2017/10/20 | Archive version V9 Released. These data are updated. |
| 2017/08/30 | Archive version V8 Released. These data are updated. |
| 2017/04/19 | Archive version V7 Released. These data are updated. |
| 2017/03/07 | Archive version V6 Released. These data are updated. |
| 2016/12/09 | Archive version V5 Released. These data are updated. |
| 2016/11/01 | Archive version V4 Released. These data are updated. |
| 2016/10/18 | Archive version V3 Released. These data are updated. |
| 2016/08/01 | Archive version V2 Released. These data are updated. |
| 2016/06/24 | ChIP-Atlas English archive site is opened. (Archive version V1) |
| 2015/12/01 | ChIP-Atlas (http://chip-atlas.org/) is opened. |
5. Literature
-6. Contact address
When you have any question about "ChIP-Atlas", contact the following:Shinya Oki
Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine
Medical Innovation Center, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
E-mail: oki[dot]shinya[dot]3w[at]kyoto-u[dot]ac[dot]jp