The transcriptome is the set of all RNA molecules, including Messenger RNA mRNA , Ribosomal RNA rRNA , Transfer RNA tRNA , and other non coding RNA produced in one or a population of cell biology cells . Scope The term can be applied to the total set of transcripts in a given organism , or to the specific subset of transcripts present in a particular cell type. Unlike the genome , which is roughly fixed for a given cell line excluding mutation s , the transcriptome can vary with external environmental conditions. Because it includes all mRNA transcripts in the cell, the transcriptome reflects the gene s that are being actively gene expression expressed at any given time, with the exception of mRNA degradation phenomena such as attenuator genetics transcriptional attenuation . The study of transcriptomics , also referred to as expression profiling , examines the expression level of mRNAs in a given cell population, often using high throughput techniques based on DNA microarray technology. The use of next generation sequencing technology to study the transcriptome at the nucleotide level is known as RNA Seq . ref Wang Methods of construction There are two general methods of creating transcriptomes ... whose transcriptome is being studied or of a closely related species. The other approach, de novo transcriptome assembly , utilizes algorithms built into assembly software to generate transcripts from .... A number of organism specific transcriptome databases have been constructed and annotated to aid ... Relation to proteome Further Proteome The transcriptome can be seen as a precursor for the proteome ... antisense Antisense Transcription in the Mammalian Transcriptome by the RIKEN Genome Exploration Research ... B, Kinzler KW. Characterization of the yeast transcriptome. Cell. 1997 Jan 24 88 2 243 51. note ... transcriptome using Genevestigator. BMC Bioinformatics 7 311 note Assou cite doi 10.1093 humupd ... ca Transcriptoma de Transkriptom es Transcriptoma fr Transcriptome ko id Transkriptomika it Trascrittoma ... more details
Orphan date March 2012 unreferenced date August 2011 Salivary transcriptome also known as saliva transcriptome defines all the mRNA , rRNA , tRNA and non coding RNA present in the saliva . Category Body fluids health stub ... more details
De novo transcriptome assembly is the method of creating a transcriptome without the aid of a reference genome . Introduction Before the development of de novo transcriptome assembly, transcriptome information ..., J.I. 2010. Optimization of de novo transcriptome assembly from next generation sequencing data ..., M. 2011. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker ... of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome ..., V., et al. 2011. De novo assembly and characterization of a maternal and developmental transcriptome .... 2011. Reptilian transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida ... , parasitism , and asexual reproduction . De novo transcriptome assembly is often the preferred ... gene expression studies. Prior to the development of transcriptome assembly computer programs, transcriptome ... . ref name Birol cite journal last Birol, I., et al year 2009 title De novo transcriptome assembly ... as actual protein isoforms. Transcriptome vs. genome assembly Unlike genome sequence coverage levels which can vary randomly as a result of repeat content in non coding intron regions of DNA transcriptome ... in transcriptome assembly contigs usually correspond to spliced isoforms , or minor variation among .... A number of assembly programs are available see De novo transcriptome assembly Assemblers Assemblers . Although these programs have been generally successful in assembling genomes, transcriptome assembly ... of repetitive sequences and thus be masked , for a transcriptome, they may indicate abundance. In addition, unlike genome sequencing, transcriptome sequencing can be strand specific, due to the possibility ... and tease apart all splicing isoforms. ref Martin, J.A. and Wang, Z. 2011. Next generation transcriptome ... and molecular interaction networks captured in the transcriptome. ref KEGG PATHWAY Database ... Oases de novo transcriptome assembler for very short reads . http www.ebi.ac.uk zerbino oases ref ... more details
File Digital Transcriptome Sequencing.jpg thumb 400px Fig 1. Digital Transcriptome Subtraction Digital transcriptome subtraction DTS is a bioinformatics method to detect the presence of novel pathogen transcripts through computational removal of the host sequences. DTS is the direct in silico analogue of the Wet laboratory wet lab approach Representational Difference Analysis Representational Difference Analysis RDA , and is made possible by unbiased high throughput sequencing and the availability of a high quality, annotated reference genome of the host. The method specifically examines the etiological agent of infectious diseases and is best known for discovering Merkel cell polyomavirus Merkel cell polymavirus , the suspect causative agent in Merkel cell carcinoma . ref name MCV cite journal last Feng H, Shuda M, Chang Y, Moore PS. title Clonal integration of a polyomavirus in human Merkel cell carcinoma. journal Science year 2008 month Jan volume 319 series 5866 pages 1096 1100 pmid 18202256 doi 10.1126 science.1152586 pmc 2740911 ref History Using computational subtraction to discover novel pathogens was first proposed in 2002 by Meyerson et al. ref name computational subtraction cite journal last Weber G, Shendure J, Tanenbaum DM, Church GM, Meyerson M. title Identification of foreign gene sequences by transcript filtering against the human genome. journal Nat Genet year 2002 ... 329 335 pmid 12659816 doi 10.1016 S0888 7543 02 00043 5 ref In 2007, the term Digital Transcriptome ... Transcriptome Subtraction by Using Short Sequence Tags To Search for Tumor Viruses in Conjunctival .... Subtracted sequences typically include RefSeq Reference human transcriptome eliminates any known ... last Chang Y, Moore PS title New Pathogen Discovery Digital Transcriptome Subtraction url http www.tumorvirology.pitt.edu ... transcripts in 1 million , ref name MCV it is unlikely to generate a transcriptome based on the original ... and Bradford Hill criteria . Must have a highly reliable, complete reference transcriptome for the organism ... more details
Orphan date February 2011 infobox biodatabase title H DBAS logo File Database.png description alternative splicing database of completely sequenced and manually annotated full length cDNAs scope organism center laboratory author Jun ichi Takeda pmid Takeda & al. 2007 ref name pmid17130147 released 2006 standard format url http jbirc.jbic.or.jp h dbas download webservice sql sparql webapp standalone license versioning frequency curation bookmark version The Human transcriptome DataBase for Alternative Splicing H DBAS is a database of Alternative splicing alternatively spliced human transcripts based on H Invitational . ref name pmid17130147 cite journal quotes yes last Takeda first Jun ichi authorlink coauthors Suzuki Yutaka, Nakao Mitsuteru, Kuroda Tsuyoshi, Sugano Sumio, Gojobori Takashi, Imanishi Tadashi year 2007 month Jan title H DBAS alternative splicing database of completely sequenced and manually annotated full length cDNAs based on H Invitational journal Nucleic Acids Res. volume 35 issue Database issue pages D104 9 publisher location England issn pmid 17130147 doi 10.1093 nar gkl854 bibcode oclc id url pmc 1716722 language eng format accessdate laysummary laysource laydate quote ref See also Alternative splicing References references External links http jbirc.jbic.or.jp h dbas . Category Biological databases Category Gene expression Category Spliceosome Category RNA splicing Biodatabase stub ... more details
Orphan date February 2009 Mergeto Meiosis date January 2012 Meiome is the term used in functional genomics for meiotic transcriptome . ref http www.horticulture.umn.edu Changbin Chen.html ref ref http www.agwine.adelaide.edu.au plant pbg gm ref Meiosis is a key feature for all sexual reproducing eukaryote s in which homologous chromosome pairing, synapse and recombination are unique. Since meiosis in most organisms occur in a short time period, study of meiotic transcript profiling is extremely hard due to the challenge of isolation of meiotic cells. There are a list of groups studying on meiotic transcriptome using high throughput techniques such as microarray and sequencing technologies. Meiome is the way to study transcript profiling using mRNA isolated from enriched meiotic cells meiocyte s . Currently there are two major approaches to understand the RNA accumulation in meiocytes 1 RNA seq and 2 Microarray. The RNA seq tech is more powerful for whole transcriptome analysis, the available analyzers such as Illumina Genome Analyzer 2 and Roche 454 analyzer made this approach more powerful. References Reflist Category Cellular processes Category Molecular genetics ... more details
Orphan date April 2012 Expressome refers to the whole set of gene expression in a Cell biology cell , tissue, organ, organisms, and species. Expressome is a slightly larger concept than transcriptome . Transcriptome is the set of transcripts, while expressome includes transcripts, protein s and other ligand s how much concentration . See also Bioinformatics DNA microarray Gel electrophoresis Mass spectrometry Protein sequencing Systems biology Expressomics List of omics topics in biology External links http bioinformatics.oupjournals.org Bioinformatics Journal Category Gene expression biology stub ko ... more details
Orphan date January 2011 infobox biodatabase title TranspoGene and microTranspoGene logo File Database.png description Transposon transposed elements influence on the transcriptome scope organism center laboratory author Asaf Levy pmid Levy & al. 2008 ref name pmid17986453 released 2007 standard format url http transpogene.tau.ac.il download http transpogene.tau.ac.il download.html download webservice sql sparql webapp standalone license versioning frequency curation bookmark version TranspoGene is a database of Transposon transposed elements located inside Translation biology protein coding genes of seven species. ref name pmid17986453 cite journal quotes yes last Levy first Asaf authorlink coauthors Sela Noa, Ast Gil year 2008 month Jan title TranspoGene and microTranspoGene transposed elements influence on the transcriptome of seven vertebrates and invertebrates journal Nucleic Acids Res. volume 36 issue Database issue pages D47 52 publisher location England issn pmid 17986453 doi 10.1093 nar gkm949 bibcode oclc id url pmc 2238949 language eng format accessdate laysummary laysource laydate quote ref See also Transposon References references External links http transpogene.tau.ac.il Category Biological databases Category Mobile genetic elements Biodatabase stub ... more details
RNA seq , also called Whole Transcriptome Shotgun Sequencing ref name morin2008 cite journal journal ... J.M. Jones, and Marco A. Marra. title Profiling the HeLa S3 transcriptome using randomly primed ..., Barrette T, Palanisamy N, Chinnaiyan AM title Transcriptome Sequencing to Detect Gene Fusions in Cancer ... with efficient ways to measure transcriptome data experimentally, allowing them to get information ... , cap analysis gene expression CAGE and massively parallel signature sequencing MPSS . Transcriptome ... HE, Manning JM, McKernan KJ, Grimmond SM. title Stem cell transcriptome profiling via massive ... Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS title SNP discovery via 454 transcriptome sequencing .... Studies including portions of the transcriptome outside poly A RNAs have shown that when using poly ... increases the capacity to retrieve data from the remaining portion of the transcriptome. The next ... 454 Sequencing ref name seq454 rnaseq http www.454.com applications transcriptome sequencing.asp ... RNA conversion to cDNA or other biasing sample manipulations such as ligation and amplification. Transcriptome ..., special attention is needed when alignment of a transcriptome to a genome, mainly when dealing with genes ... read alignment , and recently specialized algorithms for transcriptome alignment have been developed ... approach Prior to RNA seq, DNA microarrays were unchallenged as the experiment of choice for transcriptome ... via RNA seq to the extent at which a sequence is retrieved. Transcriptome studies in yeast ref ... and characterized as an expressed gene. When the transcriptome is fragmented prior to cDNA synthesis ... for digital transcriptome analysis Application to an androgen sensitive prostate cancer model ... variation discovery See also single nucleotide polymorphism Transcriptome single nucleotide variation ... the transcriptome analysis, around 7000 single nucleotide polymorphisms SNPs were recognized. Following ... SNPs covering more than 2400 maize genes. This impressive transcriptome analysis is currently being ... more details
The bibliome is the totality of biological text text corpus corpus . This term was coined around 2000 in EBI European Bioinformatics Institute to denote the importance of biological text information. Similar terms that have been less frequently used are literaturome and textome . By approximate analogy to widely used terms like genome, metabolome, proteome, and transcriptome, this ome would properly refer to the literature of a specified or contextually implied field, hence biological bibliome , political bibliome , etc. However the term has not yet been applied outside the biological and medical sciences so it currently by default applies just to the biomedical fields. It would make little sense to apply it to a particular body of texts such as MEDLINE, despite a natural analogy that might seem to suggest this the terms genome, proteome, metabolome, and transcriptome all usually assume a specific organism or cell set and except for genome a specific time point. The reason following this analogy would make little sense is that there is already an established term for this purpose, corpus . From the bibliome, biologist s and computer scientist s datamining datamine to discover new gene gene target s and drug s. Bibliomics is the bioinformatics study of bibliome. Bibliome is not a pseudoome because it is a useful concept that is used by bioinformatists. Online applications http bitem.hesge.ch content eagli eagle eye EAGLi the Engine for question Answering in Genomic Literature a terminology powered Gene Ontology , Swiss Prot keywords... biomedical retrieval engine for MEDLINE. GOCat An Automatic GO Categorizer Browser to help Functional Annotation out of Biomedical Texts also useful to functionally characterize protein and gene names lists generated by high throughput experiments http www.geneontology.org GO.tools.annotation.shtml gocat External links http bioie.ldc.upenn.edu Mining the Bibliome cite journal last Grivell first Les date March 15, 2002 title Mining the ... more details
PAR CLIP ref name pmid20371350 cite journal author Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. title Transcriptome wide identification of RNA binding protein and microRNA target sites by PAR CLIP. journal Cell volume 141 issue 1 pages 129 141 year 2010 pmid 20371350 doi 10.1016 j.cell.2010.03.009 pmc 2861495 ref Photoactivatable Ribonucleoside Enhanced Crosslinking and Immunoprecipitation is a novel method, used for identifying the binding sites of cellular RNA binding proteins RBPs and microRNA containing ribonucleoprotein complexes miRNPs . The method relies on the incorporation of photoreactive ribonucleoside analogs, such as 4 thiouridine 4 SU and 6 thioguanosine 6 SG into nascent RNA transcripts by living cells. Irradiation of the cells by UV light of 365 nm induces efficient crosslinking of photoreactive nucleoside labeled cellular RNAs to interacting RBPs. Immunoprecipitation of the RBP of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. The isolated RNA is converted into a cDNA library and deep sequenced using next generation sequencing technology ref name pmid20371350 ref Cite pmid 20644507 ref . Recently, PAR CLIP have been applied to determine the transcriptome wide binding sites of several known RBPs and microRNA containing ribonucleoprotein complexes at high resolution ref name pmid20371350 ref name pmid21037263 cite journal author Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. title starBase a database for exploring microRNA mRNA interaction maps from Argonaute CLIP Seq and Degradome Seq data. journal Nucl. Acids Res. volume 39 issue Database issue pages D202 D209 year 2011 pmid 21037263 doi 10.1093 nar gkq1056 pmc 3013664 ref . External links http starbase.sysu.edu.cn starBase database a database for exploring protein RNA and miRNA target interactions from PAR CLIP CLIP Seq , HITS C ... more details
Refimprove date December 2009 italic title In general usage, de novo is a Latin expression meaning from the beginning, afresh, anew, beginning again. It is used in De novo search , signifying the start of a new or repeated from the start algorithm in computer science, discrete and computational geometry, and in particular, a packing problem . De novo transcriptome assembly De novo transcriptome assembly , the method of creating a transcriptome without a reference genome De novo synthesis De novo synthesis of complex molecules from simple molecules in biochemistry Trial de novo , or a new trial in the legal system In the Appeals Court Standard of Review, the Appeals Court, based upon Rules of Appellant Procedure, must review non jury cases de novo to determine if the trial judge came to a reasonable conclusion. In Federal and most United States courts that rule is handled under rule 13 of the court rules. In issues of witness credibility, on de novo review, the determination of the trial court is given great weight. Conclusions of law are reviewed de novo with no presumption of correctness. ref Supreme Court of Tennessee, at Nashville Union Carbide Corp. v. Huddleston , 854 S.W.2d 87, 91 ref De novo bank, a state bank that has been in operation for five years or less In bioinformatics , de novo is a form of sequencing , as in De novo protein structure prediction de novo peptide sequencing . De novo may also be a term used to define methods for making predictions about biological features using only a computational model without extrinsic comparison to existing data. In this context, it may be sometimes interchangeable with the Latin term ab initio . De novo mutation , a genetic mutation that neither parent possessed nor transmitted. In financial terminology, numbers reported by newly founded companies especially the financial services industry are qualified as de novo , to distinguish them from older companies. For example, growth de novo means growth of newly starte ... more details
italic title Taxobox name Fasciola image Fasciola hepatica.JPG image caption Fasciola hepatica regnum Animal ia phylum Platyhelminthe s classis Trematoda subclassis Digenea ordo Echinostomida subordo Echinostomata familia Fasciolidae genus Fasciola genus authority Carl Linnaeus Linnaeus , 1758 subdivision ranks Species subdivision Fasciola is a genus of trematode s which includes economically important parasite species. Members of genus Fasciola belongs to liver flukes . They causes the disease fasciolosis . Species Fasciola hepatica Fasciola gigantica Fasciola jacksoni Hybrid biology hybrid or Introgression introgressed populations of Fasciola gigantica Fasciola hepatica also exist. ref Young N. D., Jex A. R., Cantacessi C., Hall R. S., Campbell B. E. et al. 2011 . A Portrait of the Transcriptome of the Neglected Trematode, Fasciola gigantica Biological and Biotechnological Implications . PLoS Neglected Tropical Diseases 5 2 e1004. doi 10.1371 journal.pntd.0001004 . ref References reflist parasite stub Category Fasciola Category Fasciolidae Category Veterinary helminthology ar fr Fasciola la Fasciola uk Fasciola vi Fasciola ... more details
Infobox rfam Name C0299 RNA image RF00119.jpg width caption Predicted secondary structure and sequence conservation of C0299 Symbol C0299 AltSymbols Rfam RF00119 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0001263 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The C0299 RNA family consists of a group of Shigella flexneri and Escherichia coli RNA genes which are 78 bases in length and are found between the hlyE and umuD gene s. The function of this RNA is unknown. ref cite journal last Tjaden first B coauthors Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C year 2002 title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res volume 30 pages 3732&ndash 3738 pmid 12202758 doi 10.1093 nar gkf505 issue 17 pmc 137427 ref See also C0343 RNA C0465 RNA C0719 RNA References reflist 1 External links Rfam id RF00119 name C0299 RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name C0465 RNA image RF00116.jpg width caption Predicted secondary structure and sequence conservation of C0465 Symbol C0465 AltSymbols Rfam RF00116 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The C0465 RNA is a bacterial non coding RNA of 78 nucleotides in length that is found between the tar and cheW gene s in the genomes of Escherichia coli and Shigella flexneri . This ncRNA was originally identified in E.coli using microarray high density oligonucleotide probe arrays microarray ref name pmid12202758 cite journal author Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res. volume 30 issue 17 pages 3732 8 year 2002 pmid 12202758 doi 10.1093 nar gkf505 pmc 137427 ref . The function of this ncRNA is unknown. See also C0299 RNA C0343 RNA C0719 RNA References references External links Rfam id RF00116 name C0465 RNA DEFAULTSORT C0465 Rna Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name C0719 RNA image RF00117.jpg width caption Predicted secondary structure and sequence conservation of C0719 Symbol C0719 AltSymbols Rfam RF00117 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The C0719 RNA is a bacterial non coding RNA of 222 nucleotides in length that is found between the yghK and glcB gene s in the genomes of Escherichia coli and Shigella flexneri . This non coding RNA was originally identified in E.coli using microarray high density oligonucleotide probe arrays microarray. ref name pmid12202758 cite journal author Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res. volume 30 issue 17 pages 3732 8 year 2002 pmid 12202758 doi 10.1093 nar gkf505 pmc 137427 ref The function of this ncRNA is unknown. See also C0299 RNA C0343 RNA C0465 RNA References references External links Rfam id RF00117 name C0719 RNA DEFAULTSORT C0719 Rna Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name IS102 RNA image RF00124.jpg width caption Predicted secondary structure and sequence conservation of IS102 Symbol IS102 AltSymbols Rfam RF00124 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The IS102 RNA is a non coding RNA that is found in bacteria such as Shigella flexneri and Escherichia coli . The RNA is 208 nucleotide s in length and found between the yeeP and flu genes . This RNA was identified in a computational screen of E. coli . ref cite journal last Tjaden first B coauthors Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C year 2002 title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res volume 30 pages 3732&ndash 3738 pmid 12202758 doi 10.1093 nar gkf505 issue 17 pmc 137427 ref The function of this RNA is unknown. See also IS061 RNA IS128 RNA References reflist 1 External links Rfam id RF00124 name IS102 RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name IS128 RNA image RF00125.jpg width caption Predicted secondary structure and sequence conservation of IS128 Symbol IS128 AltSymbols Rfam RF00125 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0001263 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The IS128 RNA is a non coding RNA found in bacteria such as Escherichia coli and Shigella flexneri . The RNA is 209 nucleotides in length. It is found between the sseA and sseB genes . The IS128 RNA was initially identified in a computational screen of the E. coli genome. ref cite journal last Tjaden first B coauthors Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C year 2002 title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res volume 30 pages 3732&ndash 3738 pmid 12202758 doi 10.1093 nar gkf505 issue 17 pmc 137427 ref The function of this RNA is unknown. See also IS061 RNA IS102 RNA References reflist 1 External links Rfam id RF00125 name IS128 RNA Category Non coding RNA molecular cell biology stub ... more details
Orphan date February 2009 Infobox rfam Name t44 RNA image RF00127.jpg width caption Predicted secondary structure and sequence conservation of t44 Symbol t44 AltSymbols Rfam RF00127 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The T44 RNA family consists of a number of bacterial RNA genes of between 135 and 170 bases in length. ref name Tja02 cite journal last Tjaden first B coauthors Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C year 2002 title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res volume 30 pages 3732&ndash 3738 pmid 12202758 doi 10.1093 nar gkf505 issue 17 pmc 137427 ref The t44 gene has been identified in several species of gut flora enteric bacteria but homologs have also been identified in Pseudomonas and Coxiella species. The t44 gene is found between the map and rpsB genes in all species in the full alignment apart from Shigella flexneri . The function of this RNA is unknown. ref name Tja02 References reflist 1 External links Rfam id RF00127 name t44 RNA Category Non coding RNA molecular cell biology stub ... more details
refimprove date February 2008 Leucine responsive protein , or Lrp , ref name pmid17223133 cite journal author de los Rios S, Perona JJ title Structure of the Escherichia coli leucine responsive regulatory protein Lrp reveals a novel octameric assembly journal J. Mol. Biol. volume 366 issue 5 pages 1589 602 year 2007 month March pmid 17223133 pmc 1933502 doi 10.1016 j.jmb.2006.12.032 url http linkinghub.elsevier.com retrieve pii S0022 2836 06 01707 4 ref is a global regulator protein , meaning that it regulates the biosynthesis of leucine , as well as the other branched chain amino acids , valine and isoleucine . In bacteria , it is encoded by the lrp gene . Lrp alternatively activates and represses the expression of acetolactate synthase s ALS several isoenzymes . Lrp, in E. coli, along with Dam methylase DAM plays a role in the regulation of the pap operon , pylonephritis associated pili . I m too lazy busy to look up refs for this, but you can find most of them from the article Metabolic engineering of E coli for the production of valine based on transcriptome analysis and in silico gene knockout simulation by Park et al., 2007 References reflist External links MeshName Leucine Responsive Regulatory Protein Category Proteins biochemistry stub ... more details
multiple issues notability August 2011 primary sources August 2011 self published August 2011 orphan April 2011 infobox biodatabase title Full parasites logo File Database.png description full length cDNA s of apicomplexa parasites scope organism center Sam Ratulangi University laboratory Faculty of Medicine author Josef Tuda pmid Tuda & al. 2011 ref name pmid21051343 released 2010 standard format url http fullmal.hgc.jp download webservice sql sparql webapp standalone license versioning frequency curation bookmark version Full Parasites is a transcriptome database of apicomplexa parasites. ref name pmid21051343 cite journal quotes yes last Tuda first Josef authorlink coauthors Mongan Arthur E, Tolba Mohammed E M, Imada Mihoko, Yamagishi Junya, Xuan Xuenan, Wakaguri Hiroyuki, Sugano Sumio, Sugimoto Chihiro, Suzuki Yutaka year 2011 month Jan title Full parasites database of full length cDNAs of apicomplexa parasites, 2010 update journal Nucleic Acids Res. volume 39 issue Database issue pages D625 31 publisher location England issn pmid 21051343 doi 10.1093 nar gkq1111 bibcode oclc id url pmc 3013703 language eng format accessdate laysummary laysource laydate quote ref See also apicomplexa References references External links http fullmal.hgc.jp Category Biological databases Category Apicomplexa Category Gene expression Biodatabase stub ... more details
viewed at www.onekp.com samples list.php . Transcriptome vs. genome sequencing Rather than sequencing ... those regions of the genome that produce a protein product Gene coding genes the transcriptome . ref ..., but all have tens of thousands or more making the transcriptome a large collection of information ... technologies for transcriptome analysis journal Annual Review of Genomics and Human Genetics ... the two, the non EST method is known as shotgun transcriptome sequencing . ref name thirteen Transcriptome shotgun sequencing mRNA messenger RNA is collected from a sample, converted to Complementary ... so that it can be sequenced. ref name onekp ref name eleven Other than RNA Seq transcriptome shotgun sequencing , this technique has been called RNA seq and whole transcriptome shotgun sequencing WTSS ... Since only the transcriptome is being sequenced, the project will not reveal information about Regulatory ... will only be sequencing the transcriptome, whereas the human project will sequence as much of the genome ... more details
The term metallome has been introduced by R.J.P. Williams by analogy with proteome as distribution of free metal ions in every one of Cell biology cellular compartments. Subsequently, the term metallomics has been coined as the study of metallome. Szpunar 2005 defined metallomics as comprehensive analysis of the entirety of metal and metalloid species within a cell or tissue type . Therefore, metallomics can be considered a branch of metabolomics , even though the metals are not typically considered as metabolites . Hiroki Haraguchi gave an alternative definition of metallomes as metalloprotein s or any other metal containing biomolecules , and metallomics as a study of such biomolecules. In the study of metallomes the transcriptome, proteome and the metabolome will constitute the whole metallome. A study of the metallome is done to arrive at the metallointeractome The metallotranscriptome word introduced by Shanker et al. 2009 by can be ideally defined as the map of the entire transcriptome in the presence of biologically or environmentally relevant concentrations of an essential or toxic metal, respectively metallometabolome would constitute the complete pool of small metabolites in a cell at any given time and this would give rise to the whole metallointeractome and knowledge of this would be of paramount importance in comparative metallomics dealing with toxicity and drug discovery. Shanker et al. 2009 See also Bioinorganic chemistry omics Metallomics journal External links http www.rsc.org metallomics Metallomics, the journal covering the research fields related to biometals References cite journal author Mounicou, S., Szpunar, J. and Lobinski, R. title Metallomics the concept and methodology journal Chemical Society Reviews year 2009 volume 38 pages 1119&ndash 1138 doi 10.1039 b713633c pmid 19421584 issue 4 cite journal author Williams, R.J.P. title Chemical selection of elements by cells journal Coordination Chemistry Reviews year 2001 volume 216&ndash 217 pa ... more details
Portable Document Format PDF doi 10.1016 j.ydbio.2004.09.030 ref The transcriptome of P. hawaiensis ... De novo assembly and characterization of a maternal and developmental transcriptome for the emerging ... . The transcriptome data can be used for the creation of in situ probes and other experimental tools ... more details
Encyclopedia
top
