The program calculates correlation coefficients between the gene expression values in experiments (fields).

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
NAME<tab>WORD
GENEID<tab>IVALUE
TISSUECANCER0<tab>FVALUE
TISSUECANCER1<tab>FVALUE
TISSUENORMAL0<tab>FVALUE
TISSUENORMAL1<tab>FVALUE
TISSUENORMAL2<tab>FVALUE
#GROUP<tab>Cancer tissues
TISSUECANCER0
TISSUECANCER1
#ENDGROUP
#GROUP<tab>Arbitrary group
TISSUECANCER1
TISSUECANCER2
TISSUENORMAL0
TISSUENORMAL1
#ENDGROUP
END
DATA
GENE04675<tab>402<tab>6.00<tab>5.60<tab>5.97<tab>6.00<tab>6.00
GENE46890<tab>794<tab>2.77<tab>3.22<tab>5.65<tab>5.68<tab>5.68
GENE23794<tab>404<tab>5.97<tab>5.97<tab>6.00<tab>5.60<tab>5.97

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"?>
<SELECTION>
	<HEADER name="cc_Selection5">
		<DATA source="c:/data/cc.txt"/>
		<COMMENT><![CDATA["$F1 == "GEN14263" | $F12 >= 300"]]></COMMENT>
	</HEADER>
	<ELEMENTS type="GENES" count="9">
	<![CDATA[0;1;2;10;14;15;17;26;30]]>
	</ELEMENTS>
</SELECTION>

Selection for some fields (samples).

<?xml version="1.0" encoding="ISO-8859-5"?>
<SELECTION>
	<HEADER name="notterman2001_set1">
		<DATA source="c:/data/notterman2001_set1.txt"/>
		<COMMENT><![CDATA["From cc.txt data file."]]></COMMENT>
	</HEADER>
	<ELEMENTS type="FIELDS" count="10">
	  <![CDATA[0;1;2;3;5;6;7;18;19;30]]>
	</ELEMENTS>
</SELECTION>

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 fields; program will calculate correlation coefficients between gene expression values at the fields (samples) from different lists. User can also set the threshold for correlation value to select most correlated pairs of fields. The correlation coefficient is calculated for all genes available.

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 y_ki 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 r_ij is close to zero, two expression profiles are unrelated.

Spearman r - Spearman's correlation coefficient.
This correlation coefficient is computed for ranks. Let R_ki is the rank of the expression level in the experiment k of gene i (relatively to other experiments), R_kj 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 (y_ki; y_kj) 2K(K - 1) pairs considered (without self-pairing, the points in either order count as one pair). Pairs in which y_ki > y_mi and y_kj > y_mj or y_ki < y_mi and y_kj < y_mj 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 field expression data:
FieldList1\FieldList2	BC_1_tum	BC_1_tum0	BC_3_tum	BC_4_met
BC_1_tum0	0.4507	1.0000	0.5710	0.7502
BC_5_met	0.7135	0.7354	0.4533	0.8437
BC_6_tum	0.6044	0.7008	0.4573	0.8303
BC_7_tum	0.5856	0.3001	0.5085	0.3592
BC_8_met	1.0000	0.4507	0.2643	0.5407
BC_9_tum	0.8076	0.4445	0.4591	0.3603
List of gene pairs with the absolute value of the correlation coefficients above threshold (0.8076)
BC_5_met	BC_4_met	:	0.8437
BC_6_tum	BC_4_met	:	0.8303
BC_8_met	BC_1_tum	:	1.0000
BC_9_tum	BC_1_tum	:	0.8076 

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