Configuration File

The configuration file for the Experiment Package is structured as a series of tag and value pairs, separated by a “=” character, with each line of the file holding one pair.

Configuration File Tags

Tag

Description

Content

expname

Holds the name of the Experiment Package

String of text

comments

Holds brief comments for the Experiment Package

String of text

organism

Holds the organism ID related to the experiment

hsa; mmu

geneIdType

Holds the ID type for the Transcriptomic dataset

entrez; ensembl; symbol;

gene_id_column

Holds the number representing the column with the IDs in the Transcriptomic dataset

Integer Number

gene_dev_column

Holds the number representing the column with the differential expression values in the Transcriptomic dataset

Integer Number

gene_pvalue_column

Holds the number representing the column with the p-values in the Transcriptomic dataset

Integer Number

urnaIdType

Holds the ID type for the miRNomic dataset

mirbase

urna_id_column

Holds the number representing the column with the IDs in the miRNomic dataset

Integer Number

urna_dev_column

Holds the number representing the column with the differential expression values in the miRNomic dataset

Integer Number

urna_pvalue_column

Holds the number representing the column with the p-values in the miRNomic dataset

Integer Number

metaIdType

Holds the ID type for the Metabolomic dataset

keggcompound; name;

meta_id_column

Holds the number representing the column with the IDs in the Metabolomic dataset

Integer Number

meta_dev_column

Holds the number representing the column with the expression values in the Metabolomic dataset

Integer Number

meta_pvalue_column

Holds the number representing the column with the p-values in the Metabolomic dataset

Integer Number

methIdType

Holds the ID type for the Methylomic dataset

entrez; ensembl; symbol;

meth_id_column

Holds the number representing the column with the IDs in the Methylomic dataset

Integer Number

meth_dev_column

Holds the number representing the column with the differential expression values in the Methylomic dataset

Integer Number

meth_pvalue_column

Holds the number representing the column with the p-values in the Methylomic dataset

Integer Number

protIdType

Holds the ID type for the Proteomic dataset

entry; entrez; symbol;

prot_id_column

Holds the number representing the column with the IDs in the Proteomic dataset

Integer Number

prot_dev_column

Holds the number representing the column with the differential expression values in the Proteomic dataset

Integer Number

prot_pvalue_column

Holds the number representing the column with the p-values in the Proteomic dataset

Integer Number

chromaIdType

Holds the ID type for the Chromatin Status dataset

entrez; ensembl; symbol;

chroma_id_column

Holds the number representing the column with the IDs in the Chromatin Status dataset

Integer Number

chroma_dev_column

Holds the number representing the column with the differential expression values in the Chromatin Status dataset

Integer Number

chroma_pvalue_column

Holds the number representing the column with the p-values in the Chromatin Status dataset

Integer Number

An example of a fully configured .conf file is displayed below:

Structure of a .conf file of an Experiment Package with Transcriptomic, Proteomic, miRNomic, Methylomic and Metabolomic datasets associated
expname=LTED vs MCF7+
comments=ANOVA adj.p + Tukey
organism=hsa
geneIdType=entrez
gene_id_column=8
gene_dev_column=6
gene_pvalue_column=5
protIdType=entry
prot_id_column=1
prot_dev_column=4
prot_pvalue_column=3
urnaIdType=mirbase
urna_id_column=1
urna_dev_column=6
urna_pvalue_column=5
methIdType=entrez
meth_id_column=8
meth_dev_column=6
meth_pvalue_column=5
metaIdType=keggcompound
meta_id_column=8
meta_dev_column=6
meta_pvalue_column=5
chromaIdType=entrez
chroma_id_column=8
chroma_dev_column=6
chroma_pvalue_column=5

The experiment Package is named “LTED vs MCF7+” and it’s related to an experiment involving Homo sapiens cells, it has all the -omics datasets currently supported by PathLay associated to it. We can read its configuration as it follows:

  • The Transcriptomic datataset has its Entrez IDs stored in the 8th column, Effect Size values stored in the 6th column and p-values stored in the 5th column.

  • The miRNomic datataset has its mirbase IDs stored in the 1st column, Effect Size values stored in the 6th column and p-values stored in the 5th column.

  • The Metabolomic datataset has its Kegg Compound IDs stored in the 8th column, Effect Size values stored in the 6th column and p-values stored in the 5th column.

  • The Methylomic datataset has its Entrez IDs stored in the 8th column, Effect Size values stored in the 6th column and p-values stored in the 5th column.

  • The Chromatin Status dataset has its Entrez IDs stored in the 8th column, Effect Size values stored in the 6th column and p-values stored in the 5th column.

  • The Proteomic datataset has its Uniprot Entry IDs stored in the 1st column, Effect Size values stored in the 4th column and p-values stored in the 3rd column.

Note

Experiment Packages can be created and configured in your Home Page with a more intuitive approach. Once the “Save” button is clicked the .conf file will be automatically generated and saved in your home folder.