Search scheduling apparatus, program and recording medium having the same program recorded therein

• US 20080270362A1
• Filed: 10/30/2007
• Published: 10/30/2008
• Est. Priority Date: 06/20/2001
• Status: Abandoned Application

• Current Assignee: Hitachi Software Engineering Co., Ltd. (Hitachi, Ltd.)
• Original Assignee: Hitachi Software Engineering Co., Ltd. (Hitachi, Ltd.)
• Inventors: Tamura, Takuro, Yamamoto, Noriyuki, Yamaguchi, Daisuke
• Application Number:
  US11/979,038
• Publication Number:
  US 20080270362A1
• Time in Patent Office: Days
• US Class Current: 707/3
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

To provide a search scheduling apparatus which makes it possible to control influence given by a group of spots of nonspecific reaction or errors of the reaction to arrangement and search to arrange and search probe or the like having an objective characteristic among data of experimental results of an experiment using a microarray. If an expression intensity Ep(I) of a probe P(I), which hybridizes with a sample sm(X) as a search condition, that is, an expression intensity Ep(I)t of an objective probe P(I)t, is set and inputted for a desired sample sm(X) that a user wishes to search by an input/output apparatus 10, an arithmetic unit 20 finds out a microarray A(K) satisfying the search conditions based on a record of experimental results accumulated in a data set file apparatus and displays search results on the input/output apparatus 10.

Claims

1. A search scheduling program embedded in a computer readable medium comprising:

a module for inputting experimental results data of an experiment in which a target probe is applied to a microarray comprising a spot to which a probe is immobilized and for inputting a probe and an expression intensity value as search conditions;

a module for recording in a data set file various data records for search processing;

a module for preparing a data set for search preparing and updating the various data records for search processing recorded in the data set file, based on the experimental results data;

a module for searching the various data records for search processing recorded in the data set file for a probe that characteristically hybridizes with the probe inputted as a search condition at the expression intensity value as a search condition or an approximate value thereof; and

a module for defining the data set file to comprise;

a spot record containing the experimental results data;

a spot record for search containing a probe code representing the type of a probe immobilized to a microarray spot, and containing a standardized expression intensity obtained by standardizing expression intensity measurement data of the microarray spot which is the experimental results data thereby corresponding the probe code and the standardized expression intensity to each microarray spot for each array code representing identification of each microarray on which the experiment is conducted;

an interval setting record containing definition data for each value interval set by dividing a value range of the standardized expression intensity; and

an interval record for a histogram for recording the number of microarrays containing a microarray spot to which a probe having the probe code is immobilized and expressed during the experiment at a value contained in the value interval, and a unique score Up(I)(L) which quantitatively indicates how characteristic the standardized expression intensity of the value interval is, thereby corresponding the number of microarrays and the unique score to each value interval of the standardized expression intensity defined by the interval setting record, for each probe code representing the type of the probe;

wherein the module for preparing a data set for search includes;

a module for associating the probe code of the probe immobilized to the spot with the expression intensity measurement data of the spot, for each microarray spot used in the experiment, based on the experimental results data, and for recording the probe code and the expression intensity measurement data in the spot record;

a module for associating the probe code recorded in the spot record for each spot with the array code of the microarray used in the experiment, and for recording the probe code and the array code in the spot record for search;

a module for calculating the standardized expression intensity for each spot based on the expression intensity measurement data for each microarray spot used in the experiment and recorded in the spot record, associating the standardized expression intensity for each spot with the array code of the microarray and the probe code for each spot used in the experiment, and for recording the standardized expression intensity in the spot record for search; and

a module for determining, for each microarray spot used in the experiment, by using the probe code and the standardized expression intensity for each microarray spot used in the experiment and recorded in the spot record for search in association with the array code, whether or not the standardized expression intensity of the spot is contained in any of the value intervals of standardized expression intensity defined by the interval setting record;

for determining whether or not the probe code of the spot exists in the interval record for a histogram in the data set file;

for incrementing the number of microarrays having the probe code corresponding to a previously determined value interval of the interval record for a histogram in cases when the probe code exists therein whereas setting a new interval record for a histogram for the probe code of the interval record for a histogram in the data set file in cases when the probe code does not exist therein, and for calculating a unique score Up(I)(L) corresponding to each value interval of standardized expression intensity of the probe code and updating the unique score Up(I)(L) corresponding to each value interval of the interval record for a histogram of the probe code,

wherein the module for searching the various data records for search processing includes;

a module for searching the spot record for search for a probe code corresponding to the probe inputted as a search condition, and retrieving an array code and a standardized expression intensity corresponding to the retrieved probe code;

a module for calculating, for each microarray having the retrieved array code, a difference between the expression intensity inputted as a search condition and the retrieved standardized expression intensity, and calculating an expression intensity error score Sp(I)A(K) representing the possibility of similarity regarding standardized expression intensity;

for searching the interval setting record for a value interval containing the retrieved standardized expression intensity, and searching the interval record for a histogram, based on the probe code inputted as a search condition, for the unique score Up(I)(L) of the retrieved value interval; and

for calculating a difference score DSp(I)A(K) aggregating similarity/identity and characteristics with respect to the search conditions, based on the calculated expression intensity error score Sp(I)A(K) and the retrieved unique score Up(I)(L), and

a module for outputting the difference score DSp(I)A(K),

wherein, in cases when a plurality types of the probe and a plurality of the expression intensity value are inputted as search conditions, the program further comprising;

a module for calculating a difference score total TDSp(I)A(K) by adding the difference score DSp(I)A(K) calculated for each of the plurality of types of probes as search conditions, for each microarray having the array code retrieved from the spot record for search, and

a module for outputting the difference score total TDSp(I)A(K) calculated for each microarray thereby identifying the microarray or the target probe applied to the microarray on the basis of the difference score DSp(I)A(K) and the difference score total TDSp(I)A(K).

2. The search scheduling program according to claim 1, wherein, in calculating the unique score Up(I)(L) performed on the interval record for a histogram of the probe code of the probe p(I) immobilized to the spot, the number of microarrays contained in a threshold value range SA is set to be “

MS”

for a value interval SC(L), and the total number of microarrays in all value intervals is set to be “

N”

, so as to calculate the unique score Up(I)(L) of standardized expression intensity contained in the value interval SC(L) based on Expression;

Up(I)(L)=log(N/MS)

3. The search scheduling program according to claim 1, wherein, in calculating the expression intensity error score Sp(I)A(K), the standardized expression intensity of the probe p(I)m inputted as a search condition is set to be “

Ep(I)m” and

the standardized expression intensity of a probe p(I)t that corresponds to the probe p(I)m as the search condition and that is retrieved from the spot record for search is set to be “

Ep(I)A(K)t”

, so as to calculate the expression intensity error score Sp(I)A(K) based on Expression;

Sp(I)A(K)=1−

absolute(Ep(I)m−

Ep(I)A(K)t)

4. The search scheduling program according to claim 1, wherein, in calculating the difference score DSp(I)A(K), the expression intensity error score, which is calculated based on a standardized expression intensity Ep(I)m of the probe p(I)m inputted by the input apparatus as a search condition and a standardized expression intensity Ep(I)A(K)t of the a probe p(I)t that corresponds to the probe p(I)m as a search condition and that is retrieved from the spot record for search, is set to be “

Sp(I)A(K)”

, and the unique score of the standardized expression intensity Ep(I)A(K)t of the probe p(I)t is set to be “

Up(I)(L)”

, so as to calculate the difference score DSp(I)A(K) based on Expression;

D Sp(I)A(K)=Sp(I)A(K)*Up(I)(L).

5. The search scheduling program according to claim 1 wherein, in calculating the difference score total TDSp(I)A(K), the difference score calculated for each probe as a search condition for each microarray having the array code retrieved from the spot code for search is set to be “

DSp(I)A(K)”

, so as to calculate the difference score total TDSp(I)A(K) based on Expression [[17]];

TDSp(I)A(K)=Σ

[DSp(I)A(K)]