GeneCorr description

The program calculates correlation coefficients between the gene expression profiles.

Program is provided with viewer.

Data specification

The expression data for the set of genes is represented as a table, consisting of rows (usually corresponding to genes) and columns (or fields, usually corresponding to samples/tissues/experiments). Each row corresponds to expression measurements for the gene. Columns correspond to experiments/samples/tissues. However, this table may include not only expression data, but also other information related to genes, for example gene names, classifiers, etc. Therefore we will call the table columns as 'fields' in general case. In general, columns of the table could be of four basic types:
IVALUE signed integer value;
FVALUE floating point value;
WORD text without spaces inside (single word);
STRING text with spaces inside allowed.

Fields are completely defined by their basic types and names.

SelTag Input file basic format

Basic input file format should be as follows:

; May contain comment starting from the semicolon in any line of the file
#GROUP<tab>Cancer tissues
#GROUP<tab>Arbitrary group

In this example <tab> implies 'Tab' character symbol.

First lines (up to the "DATA" line) contain data format description. In this part of the file each line describes field description: field name and field basic type.

After the "DATA" line - data on each gene are represented. Each line correspond single cards. Field data are separated by 'tab' symbol. Double 'tab' is interpreted as missed data.

It is assumed in SetTag program that the expression data in the file are normalized and the expression levels of genes in experiments are comparable.

Selection files

MolQuest version of the SelTag program can also operates with other types of files, namely, selection files. These files contain information about some selected genes or samples from the large data file in SelTag format. The selection file contain: the data file name from which selection was obtained; type of selection data (genes of samples), list of selected objects (their indices in the large data file). The selection files are in the XML format. Two examples are below.

Selection for some genes.

<?xml version="1.0" encoding="ISO-8859-5"?>
	<HEADER name="cc_Selection5">
		<DATA source="c:/data/cc.txt"/>
		<COMMENT><![CDATA["$F1 == "GEN14263" | $F12 >= 300"]]></COMMENT>
	<ELEMENTS type="GENES" count="9">

Selection for some fields (samples).

<?xml version="1.0" encoding="ISO-8859-5"?>
	<HEADER name="notterman2001_set1">
		<DATA source="c:/data/notterman2001_set1.txt"/>
		<COMMENT><![CDATA["From cc.txt data file."]]></COMMENT>
	<ELEMENTS type="FIELDS" count="10">

Selection files may be selected during the SelTag execution and also used by SelTag for calculation and/or visualization. Note, each selection file is linked to large data file by its name. Selection data cannot be applied to another data file.

Program description

User should define two lists of genes, program will calculate correlation coefficients between gene expression profiles from different lists. User can also set the threshold for correlation value to select most correlated pairs.

User should provide list of fields to calculate correlation.

Three types of correlation are possible:
Pearson's r - Pearson's correlation coefficient. The Pearson product moment correlation coefficient between expression profiles i and j is calculated as follows:

where yki is the expression level of gene i in the experiment k; is the mean expression level of the gene i. Positive correlation implies that the expression levels of genes i,j are related positively, the higher expression of gene i, the higher expression of gene j. Negative correlation means that the expression levels of genes i,j are related negatively, the higher expression of gene i, the lower expression of gene j. If the rij is close to zero, two expression profiles are unrelated.

Spearman r - Spearman's correlation coefficient.
This correlation coefficient is computed for ranks. Let Rki is the rank of the expression level in the experiment k of gene i (relatively to other experiments), Rkj is the rank of the expression level in the experiment k of gene j. Then Spearman's correlation coefficient is calculated by the formula

Kendall's t - Kendall's tau correlation coefficient. To calculate Kendall's t K for data points (yki; ykj) 2K(K - 1) pairs considered (without self-pairing, the points in either order count as one pair). Pairs in which yki > ymi and ykj > ymj or yki < ymi and ykj < ymj are called concordant pairs (agreement between ranks), pairs with rank disagreement are called discordant pairs. In general, t is calculated as
t = ([number of concordant] - [number of discordant]) / total number of pairs

Example of the output data

Correlation coefficients (Spearman rank correlation) between gene expression profiles:
List1\List2	GEN30482	GEN03437	GEN30823
GEN01998	0.5657	0.4885	0.4939
GEN03687	0.7642	0.7814	0.7617
GEN24649	0.5858	0.5624	0.6399
GEN09108	0.1657	0.0949	-0.1042
GEN09514	0.4313	0.3925	0.2861
GEN02303	0.5876	0.5993	0.4568
List of gene pairs with the absolute value of the correlation coefficients above threshold (0.7722)
GEN03687	GEN03437	:	0.7814
GEN02374	GEN03437	:	0.7941
GEN02374	GEN30823	:	0.8520

First line is the header. It contains the type of the calculated correlation in parentheses. Second line is the list if gene identifiers from the List1, separated by tabulation. Next lines list data for genes for List2 separated by tabulation.