CSV files

Introduction

rNAV is able to load a network from two CSV files. This chapter describe the CSV file format supported by rNAV.

Nodes file

csv_nodes

Nodes file must contain 5 columns:

  • Node: the node identifier, must be a unique integer

  • Gender: an integer

    • 1 for mRNA
    • 2 for sRNA
  • name:

    • for mRNA, the UniprotKB gene identifier (if you want to use DAVID Chart enrichement tool), or any other name
    • for sRNA, just its name
  • length: the length of the mRNA in nucleotide

  • group: list of neighbors identifier for each mRNA. And for sRNAs, just its own identifier.

Edges file

csv_edges

  • source_id: the identifier of the source node of the edge
  • destination_id: the identifier of the destination node of the edge
  • category:
  • similarity: the similarity score given by the alignement sequence program
  • distance:
  • pValue: the P-Value given by the alignement sequence program
  • sRNA_positions: the position of the interaction defined by its start position and its end position on the sRNA (between brackets and commas separated)
  • mRNA_positions: the position of the interaction defined by its start position and its end position on the mRNA (between brackets and commas separated)
  • Database_recurrency: total number of annotations for this edge (all databases included)
  • Database identifier & database content: the number of columns depends on the number of databases interrogated for annotation. For each database this file must content 2 columns with specific names.
  1. one column for database identifier named DBID_<DB_name>
  2. the second for database annotation terms named DB_<DB_name>

csv_edges_B