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Wigwams: identifying gene modules co-regulated across multiple biological conditions

Krzysztof Polanski, Johanna Rhodes, Claire Hill, Peijun Zhang, Dafyd J. Jenkins, Steven J. Kiddle, Aleksey Jironkin, Jim Beynon, Vicky Buchanan-Wollaston, Sascha Ott, Katherine J. Denby
2013 Computer applications in the biosciences : CABIOS  
Results: Wigwams is a simple and efficient method to identify gene modules showing evidence for co-regulation in multiple time series of gene expression data.  ...  Furthermore, modules of co-regulated genes may only show tight co-expression across a subset of the time series, i.e. show condition-dependent regulation.  ...  Wigwams (Wigwams identifies genes working across multiple situations) is a simple, deterministic and efficient method capable of identifying groups of dependently co-expressed genes, termed gene modules  ... 
doi:10.1093/bioinformatics/btt728 pmid:24351708 pmcid:PMC3967106 fatcat:2cnvfqeuavfz7imquycq34xqgq

Revealing Shared and Distinct Genes Responding to JA and SA Signaling in Arabidopsis by Meta-Analysis

Nailou Zhang, Shuang Zhou, Dongyan Yang, Zhijin Fan
2020 Frontiers in Plant Science  
Strikingly, co-expression network analysis revealed that JA/SA uniquely regulated genes showing highly coordinated co-expression only in their respective treatment.  ...  To accurately classify JA/SA analogs with as few genes as possible, 87 genes, including the SA receptor NPR4, and JA biosynthesis gene AOC1 and JA response biomarkers VSP1/2, were identified by three feature  ...  Wigwams Module Mining Wigwams program (Polanski et al., 2014) was used to identify modules of co-expressed genes spanning mock, SA and JA time course datasets of PRJNA224133.  ... 
doi:10.3389/fpls.2020.00908 pmid:32670328 pmcid:PMC7333171 fatcat:jjumv2yvhrbizlvajy6nbp33rq

Learning from Co-expression Networks: Possibilities and Challenges

Elise A. R. Serin, Harm Nijveen, Henk W. M. Hilhorst, Wilco Ligterink
2016 Frontiers in Plant Science  
We analyse integrative genomics strategies used in recent studies that successfully identified candidate genes taking advantage of gene co-expression networks.  ...  As a result, biological networks provide many more applications beyond the simple visualization of co-expressed genes.  ...  gene co-expression patterns across multiple conditions.  ... 
doi:10.3389/fpls.2016.00444 pmid:27092161 pmcid:PMC4825623 fatcat:rpi5mq6nqvffloro6csony5ubu

EDUCAÇÃO EM CIÊNCIAS E A TEORIA DA ATIVIDADE CULTURAL-HISTÓRICA: CONTRIBUIÇÕES PARA A REFLEXÃO SOBRE TENSÕES NA PRÁTICA EDUCATIVA

Juliano Camillo, Cristiano Mattos
2014 Ensaio Pesquisa em Educação em Ciências  
Environmental factors and modulators (inhibitors and activators) influence an enzyme's activity and its ability to regulate chemical reactions (i.e., life's essential functions), College Board is careful  ...  The goal for this phase of the analysis was to identify a country whose standards could serve as an overall exemplar and/or to identify exemplary features across all countries that could be highlighted  ... 
doi:10.1590/1983-21172014160113 fatcat:xin35vqhqvfhbl7743xwoojcaq

Indigenous Protocol and Artificial Intelligence Position Paper [article]

Angie Abdilla, Noelani Arista, Kaipulaumakaniolono Baker, Scott Benesiinaabandan, Michelle Brown, Melanie Cheung, Meredith Coleman, Ashley Cordes, Joel Davison, Kūpono Duncan, Sergio Garzon, D. Fox Harrell (+19 others)
2020
But if I invented a new kind of LSTM module, should that module be considered 'Indigenous AI'?  ...  Walking through the night, the Little Boy finally reaches home just as dawn breaks across his village. The Little Boy's wigwam is on the farthest side of the dark and still village.  ... 
doi:10.11573/spectrum.library.concordia.ca.00986506 fatcat:omu6watjjrgc5h4l2liyqir6mi

Sabiston_columbia_0054D_16717.pdf [article]

2021
that is an expression of biological and cultural dysfunction, while strategically ignoring any examination of ongoing structures of colonial violence.  ...  This 'legacy' framework of historicizing colonial violence has created fecund conditions for (re)apprehending Indigenous bodies at the junctures of legal and medical reasoning, where questions of punishment  ...  as cultural and biological conditions of Indigenous life.  ... 
doi:10.7916/d8-0xvw-zk61 fatcat:aoir3vq4gfe3fjkzjrog4trcwu

EXPERIENTIA EST OPTIMA MAGISTRA

A Kutsenko
unpublished
, and with another,the property of any live self-regulating system mediating its resistance to environmental conditions.  ...  Man is a social being; his progress depends not only on biological, but, first of all, on the social laws. Therefore, it is formed in the presence of the public living conditions.  ...  In other words, is the conditional equivalence of form between the object and the object on the basis of the same conditional attribution to them of common ground [3, 56] .  ... 
fatcat:glfm55a5hbfezf5mgywju2insy

The Shape of Utopia: The Architecture of Radical Reform in Nineteenth-Century America

Irene Cheng
2017
and wigwams of the past. 88 Spear reminded readers that the novel architecture was a new system, designed to coordinate with a new social condition, and to be introduced "only so soon as people and  ...  If we can not introduce some true, scientific, and regulating principles, and thereby change the general modes of action, I look for no permanent improvement in the social condition."  ... 
doi:10.7916/d8kw5d6t fatcat:advdorrcgbaahhwng7dsrjxlcq

MOTHERS & DTIUCHTeRS A QUARTERLY OF CRITICISM AND R6VI6W

Thomas Atwood
unpublished
of "social co operation," which would bring together consumer and producer co ops, hous ing co ops and credit unions, and add a fur ther dimension of social service, so that the people -united in mutual  ...  Most of the speakers, but especially Ian Campbell, mentioned that order and regulation are prominent themes in Gait's writings.  ... 
fatcat:xbf35rwpdbcltdcb3ipwaaat5u