Pub Date : 2015-09-01DOI: 10.1504/IJBRA.2015.071942
Savita Sondhi, Munna Khan, R. Vijay, A. Salhan, Satish Chouhan
When a person is emotionally charged, stress could be discerned in his voice. This paper presents a simplified and a non-invasive approach to detect psycho-physiological stress by monitoring the acoustic modifications during a stressful conversation. Voice database consists of audio clips from eight different popular FM broadcasts wherein the host of the show vexes the subjects who are otherwise unaware of the charade. The audio clips are obtained from real-life stressful conversations (no simulated emotions). Analysis is done using PRAAT software to evaluate mean fundamental frequency (F0) and formant frequencies (F1, F2, F3, F4) both in neutral and stressed state. Results suggest that F0 increases with stress; however, formant frequency decreases with stress. Comparison of Fourier and chirp spectra of short vowel segment shows that for relaxed speech, the two spectra are similar; however, for stressed speech, they differ in the high frequency range due to increased pitch modulation.
{"title":"Acoustic analysis of speech under stress","authors":"Savita Sondhi, Munna Khan, R. Vijay, A. Salhan, Satish Chouhan","doi":"10.1504/IJBRA.2015.071942","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.071942","url":null,"abstract":"When a person is emotionally charged, stress could be discerned in his voice. This paper presents a simplified and a non-invasive approach to detect psycho-physiological stress by monitoring the acoustic modifications during a stressful conversation. Voice database consists of audio clips from eight different popular FM broadcasts wherein the host of the show vexes the subjects who are otherwise unaware of the charade. The audio clips are obtained from real-life stressful conversations (no simulated emotions). Analysis is done using PRAAT software to evaluate mean fundamental frequency (F0) and formant frequencies (F1, F2, F3, F4) both in neutral and stressed state. Results suggest that F0 increases with stress; however, formant frequency decreases with stress. Comparison of Fourier and chirp spectra of short vowel segment shows that for relaxed speech, the two spectra are similar; however, for stressed speech, they differ in the high frequency range due to increased pitch modulation.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.071942","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-06-06DOI: 10.1007/978-3-319-19048-8_18
Menglu Li, Micheal Cheng, Y. Ye, W. Hon, H. Ting, T. Lam, Cy Tang, Thomas K. F. Wong, S. Yiu
{"title":"Predicting RNA Secondary Structures: One-grammar-fits-all Solution","authors":"Menglu Li, Micheal Cheng, Y. Ye, W. Hon, H. Ting, T. Lam, Cy Tang, Thomas K. F. Wong, S. Yiu","doi":"10.1007/978-3-319-19048-8_18","DOIUrl":"https://doi.org/10.1007/978-3-319-19048-8_18","url":null,"abstract":"","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79980296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-06-01DOI: 10.1504/IJBRA.2015.070139
F. Hadizadeh, Jamal Shamsara
Design of selective matrix metalloproteinases (MMPs) inhibitors is still a challenging task because of binding pocket similarities and flexibility among MMPs family. To overcome this issue we try to generate a (three-dimensional quantitative structure activity relationship) 3D-QSAR model that might reflect, at least in part, the differential properties of MMP-12 and MMP-13 active sites compared to each other. The different alignment rules were applied for CoMFA/CoMSIA model development. In an approach the best docked poses were followed by alignment based on their zinc binding group. As it was suggested by comparison of CoMSIA contour maps of MMP-12 with MMP-13, the ligand based approach can find more detailed features of specificity for MMPs that have similar highly flexible active sites, than solely analysis of available crystal structures. The residues Val(194), Leu(214) and Thr(220) of MMP-13 were suggested to be investigated for flexibility upon binding of different ligands.
{"title":"Receptor-based 3D-QSAR approach to find selectivity features of flexible similar binding sites: case study on MMP-12/MMP-13","authors":"F. Hadizadeh, Jamal Shamsara","doi":"10.1504/IJBRA.2015.070139","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.070139","url":null,"abstract":"Design of selective matrix metalloproteinases (MMPs) inhibitors is still a challenging task because of binding pocket similarities and flexibility among MMPs family. To overcome this issue we try to generate a (three-dimensional quantitative structure activity relationship) 3D-QSAR model that might reflect, at least in part, the differential properties of MMP-12 and MMP-13 active sites compared to each other. The different alignment rules were applied for CoMFA/CoMSIA model development. In an approach the best docked poses were followed by alignment based on their zinc binding group. As it was suggested by comparison of CoMSIA contour maps of MMP-12 with MMP-13, the ligand based approach can find more detailed features of specificity for MMPs that have similar highly flexible active sites, than solely analysis of available crystal structures. The residues Val(194), Leu(214) and Thr(220) of MMP-13 were suggested to be investigated for flexibility upon binding of different ligands.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.070139","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-06-01DOI: 10.1504/IJBRA.2015.070115
A. Badarinath, A. Das, Sreya Mazumder, Riya Banerjee, P. Chakraborty, R. Saraswathy
A Probabilistic Neural Network (PNN) is a statistical algorithm and consists of a grouping of multi-class data. The conventional method of detection of DNA mutations by the human eye may not detect the minute variations in PCR-SSCP bands, which may lead to false positive or false negative results. The detection by photographic images may contain a blare (noise) caused during the time of photography; therefore, image processing techniques were used to reduce image noise. PCR-SSCP gels of T2DM patients (n = 100) and controls (n = 100) were initially photographed with equal ratio of pixels and later subjected to a two-stage analysis: feature extraction and PNN. The evaluation of the results was done by quality training and the accuracy was up to 95%, and the human eye analysis showed 80% mutation detection rate. This study proves to be very reliable and gives accurate and fast detection for mutation analysis in diabetes. This method could be extended for analysis in other human diseases.
{"title":"Classification of PCR-SSCP bands in T2DM by probabilistic neural network: a reliable tool","authors":"A. Badarinath, A. Das, Sreya Mazumder, Riya Banerjee, P. Chakraborty, R. Saraswathy","doi":"10.1504/IJBRA.2015.070115","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.070115","url":null,"abstract":"A Probabilistic Neural Network (PNN) is a statistical algorithm and consists of a grouping of multi-class data. The conventional method of detection of DNA mutations by the human eye may not detect the minute variations in PCR-SSCP bands, which may lead to false positive or false negative results. The detection by photographic images may contain a blare (noise) caused during the time of photography; therefore, image processing techniques were used to reduce image noise. PCR-SSCP gels of T2DM patients (n = 100) and controls (n = 100) were initially photographed with equal ratio of pixels and later subjected to a two-stage analysis: feature extraction and PNN. The evaluation of the results was done by quality training and the accuracy was up to 95%, and the human eye analysis showed 80% mutation detection rate. This study proves to be very reliable and gives accurate and fast detection for mutation analysis in diabetes. This method could be extended for analysis in other human diseases.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.070115","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-06-01DOI: 10.1504/IJBRA.2015.070113
P. Neelakanta, S. Chatterjee, M. Pavlovic
In virology context, a particular virus may prevail in different forms of serotypes (as in the case of dengue 1-4 viral strains) with common and distinct genomic features. Finding such genomic details of a serogroup is useful in knowing related information for unique vaccine designs compatible for immunity across the viral diversity. For robust comparison of genomes of serovars of a virus in order to decide on their common and differential genomic details, proposed here is a set of sequence analyses exercised side-by-side via entropy, energetic and spectral-domain methods. Results obtained thereof with dengue viral serotypes, namely DEN1, DEN2, DEN3 and DEN4, are presented. Hence, inferences on distinct as well as common features extracted are annotated and indicated for possible vaccine design applications.
{"title":"A cohesive analysis of DNA/RNA sequences via entropy, energetics and spectral-domain methods to assess genomic features across single viral diversity","authors":"P. Neelakanta, S. Chatterjee, M. Pavlovic","doi":"10.1504/IJBRA.2015.070113","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.070113","url":null,"abstract":"In virology context, a particular virus may prevail in different forms of serotypes (as in the case of dengue 1-4 viral strains) with common and distinct genomic features. Finding such genomic details of a serogroup is useful in knowing related information for unique vaccine designs compatible for immunity across the viral diversity. For robust comparison of genomes of serovars of a virus in order to decide on their common and differential genomic details, proposed here is a set of sequence analyses exercised side-by-side via entropy, energetic and spectral-domain methods. Results obtained thereof with dengue viral serotypes, namely DEN1, DEN2, DEN3 and DEN4, are presented. Hence, inferences on distinct as well as common features extracted are annotated and indicated for possible vaccine design applications.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.070113","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-06-01DOI: 10.1504/IJBRA.2015.070138
Nikita Chordia, N. Sharma, Anil Kumar
A wide variety of human population is infected with Listeria monocytogenes, which causes listeriosis, a deadly disease with mortality rate of about 30%. The major hindrance to cure listeriosis is the unavailability of specific or selectable drug targets. At present, antibiotics used to cure the disease are not specific and insufficient to manage the disease efficiently. Therefore, in order to search specific drugs, here, we used interactome analysis to search specific drug targets which may provide novel templates for drug designing having better efficacy without any potential adverse effects. The complete genome of L. monocytogenes having 2846 proteins has been analysed. We found 11 proteins as putative drug targets. The sequence and interactome analyses revealed that 11 proteins are non-homologous to human, but essential for pathogen and hence may be considered as potential therapeutic targets.
{"title":"An interactomic approach for identification of putative drug targets in Listeria monocytogenes","authors":"Nikita Chordia, N. Sharma, Anil Kumar","doi":"10.1504/IJBRA.2015.070138","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.070138","url":null,"abstract":"A wide variety of human population is infected with Listeria monocytogenes, which causes listeriosis, a deadly disease with mortality rate of about 30%. The major hindrance to cure listeriosis is the unavailability of specific or selectable drug targets. At present, antibiotics used to cure the disease are not specific and insufficient to manage the disease efficiently. Therefore, in order to search specific drugs, here, we used interactome analysis to search specific drug targets which may provide novel templates for drug designing having better efficacy without any potential adverse effects. The complete genome of L. monocytogenes having 2846 proteins has been analysed. We found 11 proteins as putative drug targets. The sequence and interactome analyses revealed that 11 proteins are non-homologous to human, but essential for pathogen and hence may be considered as potential therapeutic targets.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.070138","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-06-01DOI: 10.1504/IJBRA.2015.070140
V. V. Khrustalev, E. V. Barkovsky, V. Kolodkina, T. Khrustaleva
In this work we described a bacterial open reading frame with two different directions of nucleotide usage biases in its two parts. The level of GC-content in third codon positions (3GC) is equal to 40.17 ± 0.22% during the most of the length of Corynebacterium diphtheriae spaC gene. However, in the 3'-end of the same gene (from codon #1600 to codon #1873) 3GC level is equal to 64.61 ± 0.91%. Using original methodology ('VVTAK Sliding window' and 'VVTAK VarInvar') we approved that there is an ongoing mutational AT-pressure during the most of the length of spaC gene (up to codon #1599), and there is an ongoing mutational G-pressure in the 3′-end of spaC. Intragenic promoters predicted by three different methods may be the cause of the differences in preferable types of nucleotide mutations in spaC parts because of their autonomous transcription.
{"title":"Opposite nucleotide usage biases in different parts of the Corynebacterium diphtheriae spaC gene","authors":"V. V. Khrustalev, E. V. Barkovsky, V. Kolodkina, T. Khrustaleva","doi":"10.1504/IJBRA.2015.070140","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.070140","url":null,"abstract":"In this work we described a bacterial open reading frame with two different directions of nucleotide usage biases in its two parts. The level of GC-content in third codon positions (3GC) is equal to 40.17 ± 0.22% during the most of the length of Corynebacterium diphtheriae spaC gene. However, in the 3'-end of the same gene (from codon #1600 to codon #1873) 3GC level is equal to 64.61 ± 0.91%. Using original methodology ('VVTAK Sliding window' and 'VVTAK VarInvar') we approved that there is an ongoing mutational AT-pressure during the most of the length of spaC gene (up to codon #1599), and there is an ongoing mutational G-pressure in the 3′-end of spaC. Intragenic promoters predicted by three different methods may be the cause of the differences in preferable types of nucleotide mutations in spaC parts because of their autonomous transcription.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.070140","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-06-01DOI: 10.1504/IJBRA.2015.070141
P. Suravajhala, T. Singh
Protein-Protein Interactions (PPI) play a crucial role in deciphering function besides identifying candidates. While the experimental analysis is often time consuming involving number of experiments like pulldown assays, they are not necessarily limiting the ability to detect novel protein interactors. In this work, we discuss the role and putative interactors of SNAI2, a slug protein which is involved in the development of cancer progression. The protein interactions have been deciphered by domain pair exclusion method which gives confidence to already precluded interaction pairs. Additionally, conservation patterns of the slug protein have also been analysed by estimating site-specific evolutionary rates at structural level. Based upon the computational analysis, we consider HNF4A could be a putative candidate to study zinc finger protein slug. We believe, this candidate study augmented with structural conservation will definitely provide novel insights into the design and discovery of new interactions for zinc finger class of proteins besides providing possible clues for discovery of various cancer types associated with this class of proteins.
{"title":"Is HNF4A a candidate to study zinc finger protein slug?","authors":"P. Suravajhala, T. Singh","doi":"10.1504/IJBRA.2015.070141","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.070141","url":null,"abstract":"Protein-Protein Interactions (PPI) play a crucial role in deciphering function besides identifying candidates. While the experimental analysis is often time consuming involving number of experiments like pulldown assays, they are not necessarily limiting the ability to detect novel protein interactors. In this work, we discuss the role and putative interactors of SNAI2, a slug protein which is involved in the development of cancer progression. The protein interactions have been deciphered by domain pair exclusion method which gives confidence to already precluded interaction pairs. Additionally, conservation patterns of the slug protein have also been analysed by estimating site-specific evolutionary rates at structural level. Based upon the computational analysis, we consider HNF4A could be a putative candidate to study zinc finger protein slug. We believe, this candidate study augmented with structural conservation will definitely provide novel insights into the design and discovery of new interactions for zinc finger class of proteins besides providing possible clues for discovery of various cancer types associated with this class of proteins.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.070141","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-05-01DOI: 10.1504/IJBRA.2015.069193
Tannu Kumari, K. Pardasani
Class B GPCR family is a small group of receptors which are activated by peptides of intermediate length that range from 30 to 40 amino acid residues including hormones, neuropeptides and autocrine factors that mediate diverse physiological functions. They are involved in physiological processes like glucose homeostasis (glucagon and glucagon-like peptide-1), calcium homeostasis and bone turnover (parathyroid hormone and calcitonin), and control of the stress axis (corticotropin-releasing factor). Most of the GPCR structures and their functions are still unknown. Thus, the study of amino acid association patterns can be useful in prediction of their structure and functions. In view of above, in this paper, an attempt has been made to explore amino acid association patterns in class B GPCRs and their relationships with secondary structures and physiochemical properties. The fuzzy association rule mining is employed to take care of uncertainty due to variation in length of sequences. The association rules have been generated with the help of patterns discovered in the sequences.
{"title":"Mining amino acid association patterns in class B GPCRs","authors":"Tannu Kumari, K. Pardasani","doi":"10.1504/IJBRA.2015.069193","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.069193","url":null,"abstract":"Class B GPCR family is a small group of receptors which are activated by peptides of intermediate length that range from 30 to 40 amino acid residues including hormones, neuropeptides and autocrine factors that mediate diverse physiological functions. They are involved in physiological processes like glucose homeostasis (glucagon and glucagon-like peptide-1), calcium homeostasis and bone turnover (parathyroid hormone and calcitonin), and control of the stress axis (corticotropin-releasing factor). Most of the GPCR structures and their functions are still unknown. Thus, the study of amino acid association patterns can be useful in prediction of their structure and functions. In view of above, in this paper, an attempt has been made to explore amino acid association patterns in class B GPCRs and their relationships with secondary structures and physiochemical properties. The fuzzy association rule mining is employed to take care of uncertainty due to variation in length of sequences. The association rules have been generated with the help of patterns discovered in the sequences.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.069193","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-05-01DOI: 10.1504/IJBRA.2015.069198
V. Binu, N. Nair, Prasad K. Manjunatha, M. Kalesh
In a cDNA microarray experiment, the final measurement is intensity ratio at a spot in the microarray chip. The objective of the present study is to estimate the uncertainty associated with the final intensity ratio at each spot in cDNA microarray chips and also to explore the role of pixel intensity correlations in statistical inferences of gene expression levels. We estimate uncertainty at each spot using the theory of error propagation under two different situations: (1) when there is no correlation between pixel intensities and (2) when the pixel intensities are positively correlated. The inverses of these estimated uncertainties are used as weights in downstream analysis to test the significance of each gene. The analysis was verified on a data downloaded from the GEO database. Our study shows that the uncertainty and statistical inference of gene expression levels depend on correlation between pixel intensities within a spot.
{"title":"Impact of pixel intensity correlations on statistical inferences of expression levels in cDNA microarray experiments","authors":"V. Binu, N. Nair, Prasad K. Manjunatha, M. Kalesh","doi":"10.1504/IJBRA.2015.069198","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.069198","url":null,"abstract":"In a cDNA microarray experiment, the final measurement is intensity ratio at a spot in the microarray chip. The objective of the present study is to estimate the uncertainty associated with the final intensity ratio at each spot in cDNA microarray chips and also to explore the role of pixel intensity correlations in statistical inferences of gene expression levels. We estimate uncertainty at each spot using the theory of error propagation under two different situations: (1) when there is no correlation between pixel intensities and (2) when the pixel intensities are positively correlated. The inverses of these estimated uncertainties are used as weights in downstream analysis to test the significance of each gene. The analysis was verified on a data downloaded from the GEO database. Our study shows that the uncertainty and statistical inference of gene expression levels depend on correlation between pixel intensities within a spot.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.069198","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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