ABOUT RIVER  

  ABOUT

  RIVER is an open web server for mining multimodal gene-directed regulatory interactions. Its web-server enables interactive exploration of multimodal regulatory interactions that are currently categorised into three modalities: Activity-By-Contact (ABC) for enhancer-gene maps, Promoter Capture Hi-C (PCHi-C), and Quantitative Trait Loci (QTL). Genes involved in regulatory interactions are annotated with a range of ontologies on functions (Gene Ontology), phenotypes (Human Phenotype Ontology), diseases (Mondo Disease Ontology), and protein domains (SCOP, Pfam, and InterPro). RIVER offers data-mining capabilities that are inclusive of the non-coding genome, summarised below:
  •  Search: Users can input keywords to explore the resource, which returns context-specific pages and gene-specific pages related to the query.
  •  Browse: Users can navigate through varied contexts such as organs, tissues, and cell types to interactively explore their respective regulatory interactions.
  •  RI2Genes: This capability enables users to identify candidate regulatory genes from their input data by mining the resource.

  Please consult  User Manual giving step-by-step instructions on how to use the RIVER resource effectively. This work has received fundings from various sources: National Natural Science Foundation of China [32170663] and Innovative Research Team of High-Level Local Universities in Shanghai.

  MYSQL

Content_dbRIVER_202411.sql.gz    contains 5 tables, with the schema outlined below:

USE


  Restore the RIVER MySQL database 
# Enter password if prompted
mysql -u root -p -e "create database RIVERdb;"
gunzip < Content_dbRIVER_202411.sql.gz | mysql -u root -p dbRIVER
  Show tables 
mysql> USE dbRIVER;
mysql> SHOW tables;
+------------------------+
| Tables_in_dbriver      |
+------------------------+
| context_info           |
| gene_info              |
| gene_term              |
| gr_info                |
| regulatory_interaction |
+------------------------+
  Extract genomic regions that interact with the gene 'IL17A' (based on the modality 'PCHiC') 
mysql> SELECT a.CID, b.label, a.GR, a.Gene, a.Score 
FROM regulatory_interaction AS a, context_info AS b 
WHERE a.CID=b.CID AND b.Modal='PCHiC' AND a.Gene='IL17A'
ORDER BY a.Score DESC;
+-------+-----------------------------------------------+------------------------+-------+--------------+
| CID   | label                                         | GR                     | Gene  | Score        |
+-------+-----------------------------------------------+------------------------+-------+--------------+
| C0081 | Aorta (PMID31501517)                          | chr6:50715234-50721151 | IL17A |   0.00886063 |
| C0088 | Fat (PMID31501517)                            | chr6:52021964-52028582 | IL17A |   0.00793775 |
| C0080 | AdrenalGland (PMID31501517)                   | chr6:50138944-50145136 | IL17A |   0.00741363 |
| C0126 | hippocampal (PMID31367015)                    | chr6:52107437-52120696 | IL17A |   0.00652897 |
| C0123 | Trophoblast (PMID31501517)                    | chr6:52121367-52124792 | IL17A |   0.00572892 |
| C0112 | Pancreas (PMID31501517)                       | chr6:52028583-52033567 | IL17A |   0.00566848 |
| C0123 | Trophoblast (PMID31501517)                    | chr6:52874476-52880638 | IL17A |   0.00491858 |
| C0081 | Aorta (PMID31501517)                          | chr6:51983487-51987113 | IL17A |   0.00432594 |
| C0112 | Pancreas (PMID31501517)                       | chr6:51976923-51980357 | IL17A |   0.00291745 |
| C0110 | Nonactivated_total_CD4_T_cells (PMID27863249) | chr6:52507448-52510680 | IL17A |   0.00215937 |
| C0082 | Bladder (PMID31501517)                        | chr6:52097457-52102314 | IL17A |   0.00208858 |
| C0123 | Trophoblast (PMID31501517)                    | chr6:51930792-51937411 | IL17A |   0.00140648 |
| C0107 | Naive_CD4_T_cells (PMID27863249)              | chr6:52516121-52519136 | IL17A |   0.00116485 |
| C0110 | Nonactivated_total_CD4_T_cells (PMID27863249) | chr6:52548793-52551154 | IL17A |   0.00109584 |
| C0097 | LCL (PMID31501517)                            | chr6:50706937-50711709 | IL17A |   0.00102056 |
| C0079 | Activated_total_CD4_T_cells (PMID27863249)    | chr6:52527279-52528288 | IL17A |  0.000919697 |
| C0111 | Ovary (PMID31501517)                          | chr6:52097457-52102314 | IL17A |  0.000908583 |
| C0108 | Naive_CD8_T_cells (PMID27863249)              | chr6:52516121-52519136 | IL17A |  0.000851565 |
| C0122 | Total_CD8_T_cells (PMID27863249)              | chr6:52516121-52519136 | IL17A |  0.000743387 |
| C0079 | Activated_total_CD4_T_cells (PMID27863249)    | chr6:52564858-52565095 | IL17A |  0.000726709 |
| C0121 | Total_CD4_T_cells (PMID27863249)              | chr6:52529945-52533082 | IL17A |  0.000650316 |
| C0079 | Activated_total_CD4_T_cells (PMID27863249)    | chr6:52565096-52568603 | IL17A |  0.000545248 |
| C0109 | Neutrophils (PMID27863249)                    | chr6:50770604-50780906 | IL17A |  0.000543862 |
| C0109 | Neutrophils (PMID27863249)                    | chr6:50796768-50800786 | IL17A |  0.000511279 |
| C0079 | Activated_total_CD4_T_cells (PMID27863249)    | chr6:52483390-52486722 | IL17A |  0.000504013 |
| C0123 | Trophoblast (PMID31501517)                    | chr6:51998371-52001727 | IL17A |  0.000475964 |
| C0122 | Total_CD8_T_cells (PMID27863249)              | chr6:52582960-52583875 | IL17A |  0.000459409 |
| C0123 | Trophoblast (PMID31501517)                    | chr6:52168413-52176918 | IL17A |  0.000450113 |
| C0099 | Liver (PMID31501517)                          | chr6:51365528-51370740 | IL17A |  0.000427498 |
| C0108 | Naive_CD8_T_cells (PMID27863249)              | chr6:52564858-52565095 | IL17A |  0.000414165 |
| C0108 | Naive_CD8_T_cells (PMID27863249)              | chr6:52551155-52557252 | IL17A |  0.000373828 |
| C0107 | Naive_CD4_T_cells (PMID27863249)              | chr6:52507448-52510680 | IL17A |   0.00034523 |
| C0110 | Nonactivated_total_CD4_T_cells (PMID27863249) | chr6:52557253-52561729 | IL17A |  0.000311453 |
| C0110 | Nonactivated_total_CD4_T_cells (PMID27863249) | chr6:52564858-52565095 | IL17A |  0.000303343 |
| C0121 | Total_CD4_T_cells (PMID27863249)              | chr6:52582960-52583875 | IL17A |  0.000257019 |
| C0122 | Total_CD8_T_cells (PMID27863249)              | chr6:52506678-52507447 | IL17A |  0.000244341 |
| C0109 | Neutrophils (PMID27863249)                    | chr6:50766439-50770603 | IL17A |  0.000182812 |
| C0121 | Total_CD4_T_cells (PMID27863249)              | chr6:52551155-52557252 | IL17A |  0.000175933 |
| C0127 | motor (PMID31367015)                          | chr6:52120697-52122033 | IL17A |  0.000166591 |
| C0110 | Nonactivated_total_CD4_T_cells (PMID27863249) | chr6:52583876-52584149 | IL17A |  0.000141738 |
| C0107 | Naive_CD4_T_cells (PMID27863249)              | chr6:52582960-52583875 | IL17A |  0.000110967 |
| C0122 | Total_CD8_T_cells (PMID27863249)              | chr6:52474654-52478765 | IL17A | 0.0000768145 |
| C0079 | Activated_total_CD4_T_cells (PMID27863249)    | chr6:52608673-52609968 | IL17A | 0.0000613927 |
| C0110 | Nonactivated_total_CD4_T_cells (PMID27863249) | chr6:52537239-52538716 | IL17A | 0.0000469573 |
| C0110 | Nonactivated_total_CD4_T_cells (PMID27863249) | chr6:52565096-52568603 | IL17A | 0.0000382299 |
| C0121 | Total_CD4_T_cells (PMID27863249)              | chr6:52507448-52510680 | IL17A |  0.000033339 |
+-------+-----------------------------------------------+------------------------+-------+--------------+

context_info


  A table about contexts    Table_context_info.txt.gz 
mysql> DESC context_info;
+----------+---------------------------+------+-----+---------+-------+
| Field    | Type                      | Null | Key | Default | Extra |
+----------+---------------------------+------+-----+---------+-------+
| CID      | varchar(5)                | NO   | PRI | NULL    |       |
| Modal    | enum('ABC','PCHiC','QTL') | NO   | MUL | NULL    |       |
| Context  | varchar(100)              | NO   | MUL | NULL    |       |
| num_ri   | int unsigned              | NO   |     | 0       |       |
| num_gene | int unsigned              | NO   |     | 0       |       |
| label    | varchar(100)              | NO   | MUL | NULL    |       |
| pmid     | int unsigned              | NO   |     | 0       |       |
+----------+---------------------------+------+-----+---------+-------+
  • The CID column is the context ID
  • The Modal column is the modality for regulatory interactions
  • The Context column is the name of contexts
  • The num_ri column is the number of regulatory interactions
  • The num_gene column is the number of genes
  • The label column is the human-friendly description of contexts
  • The pmid column is PubMed ID for this published dataset

regulatory_interaction


  A table about regulatory interactions    Table_regulatory_interaction.txt.gz 
mysql> DESC ri;
+-------+--------------+------+-----+---------+----------------+
| Field | Type         | Null | Key | Default | Extra          |
+-------+--------------+------+-----+---------+----------------+
| CID   | varchar(5)   | NO   | PRI | NULL    |                |
| GR    | varchar(50)  | NO   | PRI | NULL    |                |
| Gene  | varchar(100) | NO   | PRI | NULL    |                |
| Score | double       | YES  |     | NULL    |                |
| auto  | int          | NO   | UNI | NULL    | auto_increment |
+-------+--------------+------+-----+---------+----------------+
  • The CID column is the context ID
  • The GR column is the genomic region
  • The Gene column is the official gene symbol
  • The Score column is the score for regulatory interactions
  • The auto column is an increasing sequence of unique numbers, collectively acting as a primary key

gr_info


  A table about genomic regions    Table_gr_info.txt.gz 
mysql> DESC gr_info;
+-------+--------------+------+-----+---------+----------------+
| Field | Type         | Null | Key | Default | Extra          |
+-------+--------------+------+-----+---------+----------------+
| GR    | varchar(50)  | NO   | PRI | NULL    |                |
| GRlen | int unsigned | NO   |     | 0       |                |
| auto  | int          | NO   | UNI | NULL    | auto_increment |
+-------+--------------+------+-----+---------+----------------+
  • The GR column is the genomic region
  • The GRlen column is the genomic region length (calculated based on GR)
  • The auto column is an increasing sequence of unique numbers, collectively acting as a primary key

gene_info


  A table about human genes    Table_gene_info.txt.gz 
mysql> DESC gene_info;
+-------------+--------------+------+-----+---------+----------------+
| Field       | Type         | Null | Key | Default | Extra          |
+-------------+--------------+------+-----+---------+----------------+
| Gene        | varchar(100) | NO   | PRI | NULL    |                |
| GeneID      | int unsigned | NO   |     | 0       |                |
| GeneLoc     | varchar(50)  | NO   |     | NULL    |                |
| GeneLen     | int unsigned | NO   |     | 0       |                |
| Description | varchar(255) | NO   |     | NULL    |                |
| auto        | int          | NO   | UNI | NULL    | auto_increment |
+-------------+--------------+------+-----+---------+----------------+
  • The Gene column is the official gene symbol
  • The GeneID column is the NCBI Gene ID
  • The GeneLoc column is the genomic location (derived from UCSC known genes)
  • The GeneLen column is the gene length (calculated based on GeneLoc)
  • The Description column is the official gene description
  • The auto column is an increasing sequence of unique numbers, collectively acting as a primary key

gene_term


  A table about gene annotations using ontology terms    Table_gene_term.txt.gz 
mysql> DESC gene_info;
+----------+--------------+------+-----+---------+----------------+
| Field    | Type         | Null | Key | Default | Extra          |
+----------+--------------+------+-----+---------+----------------+
| Gene     | varchar(100) | NO   | PRI | NULL    |                |
| Ontology | char(8)      | NO   | PRI | NULL    |                |
| TermID   | varchar(50)  | NO   | PRI | NULL    |                |
| Name     | varchar(255) | NO   |     | NULL    |                |
| auto     | int          | NO   | UNI | NULL    | auto_increment |
+----------+--------------+------+-----+---------+----------------+
  • The Gene column is the official gene symbol
  • The Ontology column is the Ontology
  • The TermID column is the ontology term ID
  • The Name column is the ontology term name
  • The auto column is an increasing sequence of unique numbers, collectively acting as a primary key