http://www.ncbi.nlm.nih.gov/pubmed/21183079
A tissue-specific atlas of mouse protein phosphorylation and expression
interesting to intersect with mouse encode in relation to TFs & gene expression – how does it relate to cell lines ?
http://www.sciencemag.org/content/325/5948/1682.abstract
Relates to the lab’s rewiring paper (Shou et al.) and should have been cited as it has the same conclusion
http://www.ncbi.nlm.nih.gov/pubmed/18668037
few genes go down substantially in prot. abundance with a fall in RNA abundance from miRNA
http://www.cell.com/developmental-cell/retrieve/pii/S1534580711001213
Expression time course comparison of orthologs, which are closer than random. Uses sigmoid approximations for gene expression levels — on & off. Discussion on purifying selection related to expression.
Some interesting terms :
http://en.wikipedia.org/wiki/Heterochrony
http://medical-dictionary.thefreedictionary.com/heterometric
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890323/?tool=pubmed
Interesting in relation to duplication, numbers of pseudogenes and gene expression levels.
http://www.pnas.org/content/106/18/7507.long
effects of polymorphisms in uORFs in the human population… perhaps worth a larger survey
Nat Commun. 2011; vol. 2 pp. 519
Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution.
Carmi S, Church GM, Levanon EY
URL – http://www.ncbi.nlm.nih.gov/pubmed/22044998?dopt=Citation
Might be interesting in relation to alu burst
Genes Dev. 2010 Dec 1; vol. 24(23) pp. 2603-14
Dynamics in the mixed microbial concourse.
Wintermute EH, Silver PA
URL – http://www.ncbi.nlm.nih.gov/pubmed/21123647?dopt=Citation
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000590
The paper describes a computational method called expression screening for extracting novel information from large amounts of experimental data sets. More precisely the authors find a series of new regulator genes for the human oxidative phosphorylation system (OxPhos). A number of 1427 non redundant microarray data sets were used as the information pool, based on the available data from NCBI Gene Expression Omnibus. The method analyses the correlation of the expression pattern between a defined set of genes in each of the microarray data set. “Genes that consistently co-express with the query gene set in many independent data sets likely have a functional role in the query pathway”. Each data set is weighted and then all the data is integrated in order to give the coexpression probability of each gene in each data set.
The method was tested successfully on the genes from the cholesterol biosysntehsis pathway. When tested on the OxPhos pathway a series of new genes emerged as being necessary for the OxPhos function. A set of five novel OxPhos genes were tested experimentally (C14orf2, USMG5, CHCHD2, SLIRP and PARK7) using knockout and qPCR assays. From these, SLIRP emerged as a gene encoding an RNA binding protein that regulates the mitochondrial RNA, more specifically affecting the mtRNA transcripts. Studies also show that mtRNA abundance affects in equal measure the stability of SLIRP proteins. CHCHD2 was also proven essential to OxPhos.
http://www.sciencemag.org/content/336/6084/1040.short
Surveyed Gly Levels in NCI-60 cell lines and correlated with cell phenotype