publication . Preprint . 2015

A novel method to enhance the sensitivity of marker detection using a refined hierarchical prior of tissue similarities

Shahin Mohammadi; Ananth Grama;
Open Access English
  • Published: 11 Jun 2015
  • Publisher: Cold Spring Harbor Laboratory
Abstract
<jats:p>Identification of biochemical processes that drive the transformation of a totipotent cell into various cell types is essential to our understanding of living systems. This complex machinery determines how tissues differ in terms of their anatomy, physiology, morphology, and, more importantly, how various cellular control mechanisms contribute to the observed similarities/ differences. Tissue-selective genes orchestrate various aspects of cellular machinery in different tissues, and are known to be implicated in a number of tissue-specific pathologies. We propose a novel statistical approach that identifies and removes the effect of universally expressed...
Subjects
free text keywords: Living systems, Cell type, Bioinformatics, Available expression, Gene, Biology, Systems biology
Funded by
NSF| Emerging Frontiers of Science of Information
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0939370
  • Funding stream: Directorate for Computer & Information Science & Engineering | Division of Computing and Communication Foundations
,
NSF| Collaborative Research: CDI-Type II: Probing Complex Dynamics of Small Interfering RNA (siRNA) Transfection by Petascale Simulations and Network Analysis
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1124962
  • Funding stream: Directorate for Biological Sciences | Division of Integrative Organismal Systems
36 references, page 1 of 3

[1] Dezso, Z., Nikolsky, Y., Sviridov, E., Shi, W., Serebriyskaya, T., Dosymbekov, D., Bugrim, A., Rakhmatulin, E., Brennan, R.J., Guryanov, A., Li, K., Blake, J., Samaha, R.R., Nikolskaya, T.: A comprehensive functional analysis of tissue speci city of human gene expression. BMC biology 6, 49 (2008). doi:10.1186/1741-7007-6-49 [OpenAIRE]

[2] Chang, C.-W., Cheng, W.-C., Chen, C.-R., Shu, W.-Y., Tsai, M.-L., Huang, C.-L., Hsu, I.C.: Identi cation of human housekeeping genes and tissue-selective genes by microarray meta-analysis. PloS one 6(7), 22859 (2011). doi:10.1371/journal.pone.0022859

[3] Souiai, O., Becker, E., Prieto, C., Benkahla, A., De las Rivas, J., Brun, C.: Functional integrative levels in the human interactome recapitulate organ organization. PloS one 6(7), 22051 (2011). doi:10.1371/journal.pone.0022051

[4] Wang, L., Srivastava, A.K., Schwartz, C.E.: Microarray data integration for genome-wide analysis of human tissue-selective gene expression. BMC genomics 11 Suppl 2, 15 (2010). doi:10.1186/1471-2164-11-S2-S15

[5] Cavalli, F.M.G., Bourgon, R., Huber, W., Vaquerizas, J.M., Luscombe, N.M.: SpeCond: a method to detect condition-speci c gene expression. Genome biology 12(10), 101 (2011). doi:10.1186/gb-2011-12-10-r101 [OpenAIRE]

[6] Teng, S., Yang, J.Y., Wang, L.: Genome-wide prediction and analysis of human tissue-selective genes using microarray expression data. BMC medical genomics 6 Suppl 1, 10 (2013). doi:10.1186/1755-8794-6-S1-S10

[7] Goh, K.-I., Cusick, M.E., Valle, D., Childs, B., Vidal, M., Barabasi, A.-L.: The human disease network. Proceedings of the National Academy of Sciences of the United States of America 104(21), 8685{90 (2007). doi:10.1073/pnas.0701361104

[8] Lage, K., Hansen, N.T., Karlberg, E.O., Eklund, A.C., Roque, F.S., Donahoe, P.K., Szallasi, Z., Jensen, T.S.t., Brunak, S.r.: A large-scale analysis of tissue-speci c pathology and gene expression of human disease genes and complexes. Proceedings of the National Academy of Sciences of the United States of America 105(52), 20870{5 (2008). doi:10.1073/pnas.0810772105

[9] Kadota, K., Ye, J., Nakai, Y., Terada, T., Shimizu, K.: ROKU: a novel method for identi cation of tissuespeci c genes. BMC bioinformatics 7, 294 (2006). doi:10.1186/1471-2105-7-294

[10] Cheng, W.-C., Tsai, M.-L., Chang, C.-W., Huang, C.-L., Chen, C.-R., Shu, W.-Y., Lee, Y.-S., Wang, T.-H., Hong, J.-H., Li, C.-Y., Hsu, I.C.: Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. BMC bioinformatics 11, 421 (2010). doi:10.1186/1471-2105-11-421

[11] Uhlen, M., Fagerberg, L., Hallstr&#x7f;om, B.M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, A.s., Kampf, C., Sj&#x7f;ostedt, E., Asplund, A., Olsson, I., Edlund, K., Lundberg, E., Navani, S., Szigyarto, C.A.-k., Odeberg, J., Djureinovic, D., Takanen, J.O., Hober, S., Alm, T., Edqvist, P.-h., Berling, H., Tegel, H., Mulder, J., Rockberg, J., Nilsson, P., Schwenk, J.M., Hamsten, M., Feilitzen, K.V., Forsberg, M., Persson, L., Johansson, F., Zwahlen, M., Heijne, G.V., Nielsen, J., Ponten, F.: Tissue-based map of the human proteome (2015). doi:10.1126/science.1260419

[12] Eisenberg, E., Levanon, E.Y.: Human housekeeping genes, revisited (2013). doi:10.1016/j.tig.2013.05.010 [OpenAIRE]

[13] Yanai, I., Benjamin, H., Shmoish, M., Chalifa-Caspi, V., Shklar, M., Ophir, R., Bar-Even, A., Horn-Saban, S., Safran, M., Domany, E., Lancet, D., Shmueli, O.: Genome-wide midrange transcription pro les reveal expression level relationships in human tissue speci cation. Bioinformatics (Oxford, England) 21(5), 650{9 (2005). doi:10.1093/bioinformatics/bti042

[14] Barber, R.D., Harmer, D.W., Coleman, R.A., Clark, B.J.: GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues. Physiological genomics 21(3), 389{95 (2005). doi:10.1152/physiolgenomics.00025.2005

[15] Abbas, A.R., Baldwin, D., Ma, Y., Ouyang, W., Gurney, A., Martin, F., Fong, S., van Lookeren Campagne, M., Godowski, P., Williams, P.M., Chan, A.C., Clark, H.F.: Immune response in silico (IRIS): immune-speci c genes identi ed from a compendium of microarray expression data. Genes and immunity 6(4), 319{31 (2005). doi:10.1038/sj.gene.6364173

36 references, page 1 of 3
Abstract
<jats:p>Identification of biochemical processes that drive the transformation of a totipotent cell into various cell types is essential to our understanding of living systems. This complex machinery determines how tissues differ in terms of their anatomy, physiology, morphology, and, more importantly, how various cellular control mechanisms contribute to the observed similarities/ differences. Tissue-selective genes orchestrate various aspects of cellular machinery in different tissues, and are known to be implicated in a number of tissue-specific pathologies. We propose a novel statistical approach that identifies and removes the effect of universally expressed...
Subjects
free text keywords: Living systems, Cell type, Bioinformatics, Available expression, Gene, Biology, Systems biology
Funded by
NSF| Emerging Frontiers of Science of Information
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0939370
  • Funding stream: Directorate for Computer & Information Science & Engineering | Division of Computing and Communication Foundations
,
NSF| Collaborative Research: CDI-Type II: Probing Complex Dynamics of Small Interfering RNA (siRNA) Transfection by Petascale Simulations and Network Analysis
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1124962
  • Funding stream: Directorate for Biological Sciences | Division of Integrative Organismal Systems
36 references, page 1 of 3

[1] Dezso, Z., Nikolsky, Y., Sviridov, E., Shi, W., Serebriyskaya, T., Dosymbekov, D., Bugrim, A., Rakhmatulin, E., Brennan, R.J., Guryanov, A., Li, K., Blake, J., Samaha, R.R., Nikolskaya, T.: A comprehensive functional analysis of tissue speci city of human gene expression. BMC biology 6, 49 (2008). doi:10.1186/1741-7007-6-49 [OpenAIRE]

[2] Chang, C.-W., Cheng, W.-C., Chen, C.-R., Shu, W.-Y., Tsai, M.-L., Huang, C.-L., Hsu, I.C.: Identi cation of human housekeeping genes and tissue-selective genes by microarray meta-analysis. PloS one 6(7), 22859 (2011). doi:10.1371/journal.pone.0022859

[3] Souiai, O., Becker, E., Prieto, C., Benkahla, A., De las Rivas, J., Brun, C.: Functional integrative levels in the human interactome recapitulate organ organization. PloS one 6(7), 22051 (2011). doi:10.1371/journal.pone.0022051

[4] Wang, L., Srivastava, A.K., Schwartz, C.E.: Microarray data integration for genome-wide analysis of human tissue-selective gene expression. BMC genomics 11 Suppl 2, 15 (2010). doi:10.1186/1471-2164-11-S2-S15

[5] Cavalli, F.M.G., Bourgon, R., Huber, W., Vaquerizas, J.M., Luscombe, N.M.: SpeCond: a method to detect condition-speci c gene expression. Genome biology 12(10), 101 (2011). doi:10.1186/gb-2011-12-10-r101 [OpenAIRE]

[6] Teng, S., Yang, J.Y., Wang, L.: Genome-wide prediction and analysis of human tissue-selective genes using microarray expression data. BMC medical genomics 6 Suppl 1, 10 (2013). doi:10.1186/1755-8794-6-S1-S10

[7] Goh, K.-I., Cusick, M.E., Valle, D., Childs, B., Vidal, M., Barabasi, A.-L.: The human disease network. Proceedings of the National Academy of Sciences of the United States of America 104(21), 8685{90 (2007). doi:10.1073/pnas.0701361104

[8] Lage, K., Hansen, N.T., Karlberg, E.O., Eklund, A.C., Roque, F.S., Donahoe, P.K., Szallasi, Z., Jensen, T.S.t., Brunak, S.r.: A large-scale analysis of tissue-speci c pathology and gene expression of human disease genes and complexes. Proceedings of the National Academy of Sciences of the United States of America 105(52), 20870{5 (2008). doi:10.1073/pnas.0810772105

[9] Kadota, K., Ye, J., Nakai, Y., Terada, T., Shimizu, K.: ROKU: a novel method for identi cation of tissuespeci c genes. BMC bioinformatics 7, 294 (2006). doi:10.1186/1471-2105-7-294

[10] Cheng, W.-C., Tsai, M.-L., Chang, C.-W., Huang, C.-L., Chen, C.-R., Shu, W.-Y., Lee, Y.-S., Wang, T.-H., Hong, J.-H., Li, C.-Y., Hsu, I.C.: Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. BMC bioinformatics 11, 421 (2010). doi:10.1186/1471-2105-11-421

[11] Uhlen, M., Fagerberg, L., Hallstr&#x7f;om, B.M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, A.s., Kampf, C., Sj&#x7f;ostedt, E., Asplund, A., Olsson, I., Edlund, K., Lundberg, E., Navani, S., Szigyarto, C.A.-k., Odeberg, J., Djureinovic, D., Takanen, J.O., Hober, S., Alm, T., Edqvist, P.-h., Berling, H., Tegel, H., Mulder, J., Rockberg, J., Nilsson, P., Schwenk, J.M., Hamsten, M., Feilitzen, K.V., Forsberg, M., Persson, L., Johansson, F., Zwahlen, M., Heijne, G.V., Nielsen, J., Ponten, F.: Tissue-based map of the human proteome (2015). doi:10.1126/science.1260419

[12] Eisenberg, E., Levanon, E.Y.: Human housekeeping genes, revisited (2013). doi:10.1016/j.tig.2013.05.010 [OpenAIRE]

[13] Yanai, I., Benjamin, H., Shmoish, M., Chalifa-Caspi, V., Shklar, M., Ophir, R., Bar-Even, A., Horn-Saban, S., Safran, M., Domany, E., Lancet, D., Shmueli, O.: Genome-wide midrange transcription pro les reveal expression level relationships in human tissue speci cation. Bioinformatics (Oxford, England) 21(5), 650{9 (2005). doi:10.1093/bioinformatics/bti042

[14] Barber, R.D., Harmer, D.W., Coleman, R.A., Clark, B.J.: GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues. Physiological genomics 21(3), 389{95 (2005). doi:10.1152/physiolgenomics.00025.2005

[15] Abbas, A.R., Baldwin, D., Ma, Y., Ouyang, W., Gurney, A., Martin, F., Fong, S., van Lookeren Campagne, M., Godowski, P., Williams, P.M., Chan, A.C., Clark, H.F.: Immune response in silico (IRIS): immune-speci c genes identi ed from a compendium of microarray expression data. Genes and immunity 6(4), 319{31 (2005). doi:10.1038/sj.gene.6364173

36 references, page 1 of 3
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publication . Preprint . 2015

A novel method to enhance the sensitivity of marker detection using a refined hierarchical prior of tissue similarities

Shahin Mohammadi; Ananth Grama;