How many human genes can be defined as housekeeping with current expression data?-1

EST data (A). Tissues are ranked from the poorly-sampled (left) to the highly-sampled (right) according to the EST data. The numbers of detected HK408 genes are plotted against the numbers of sampled ESTs for the 18 tissues (B). The sampling growth curve is fitted by Hill function () =/() with = 405.0, = 2.4, = 7.0e+10. Five tissues — muscle, ovary, heart, thymus and thyroid — are poorly sampled, primarily accounting for the absence of HK408 genes. The expression breadth of HK408 is predominantly enriched at the value 18 in the EST data (C) whereas a messy tail is observed across all breadth groups in microarray data, indicating a noisy nature and high FP rate (D).<p><b>Copyright information:</b></p><p>Taken from "How many human genes can be defined as housekeeping with current expression data?"</p><p>http://www.biomedcentral.com/1471-2164/9/172</p><p>BMC Genomics 2008;9():172-172.</p><p>Published online 16 Apr 2008</p><p>PMCID:PMC2396180.</p><p></p

Functional Categories of up-regulated and down-regulated genes in panicles, leaves, and roots

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in an elite hybrid rice cultivar () and its parental lines based on SAGE data"</p><p>http://www.biomedcentral.com/1471-2229/7/49</p><p>BMC Plant Biology 2007;7():49-49.</p><p>Published online 19 Sep 2007</p><p>PMCID:PMC2077334.</p><p></p

Differential gene expression in an elite hybrid rice cultivar () and its parental lines based on SAGE data-4

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in an elite hybrid rice cultivar () and its parental lines based on SAGE data"</p><p>http://www.biomedcentral.com/1471-2229/7/49</p><p>BMC Plant Biology 2007;7():49-49.</p><p>Published online 19 Sep 2007</p><p>PMCID:PMC2077334.</p><p></p>ion, glycolic acid oxidation, and fatty acid β-oxdidation pathways are shown. The enzymes (denotes key or rate-limiting enzymes) are: E1, fructose-1,6-bisphosphatase; E2, fructose-bisphosphate aldolase; E3, glyceraldehyde 3-phosphate dehydrogenase; E4, phosphoglycerate kinase; E5, pyruvate kinase; E6, alcohol dehydrogenase; E7, catalase; E8, acyl-CoA dehydrogenase; E9, succinyl-CoA ligase; E10, malate dehydrogenase; E11, ribulose bisphosphate carboxylase; E12, transketolase; E13, ribulose-phosphate 3-epimerase; E14, phosphoribulokinase; E15, beta-phosphoglucomutase, 1,4-alpha-glucan branching enzyme; E16, sucrose phosphate synthase; E17, sucrose synthase. Proteins and enzymes in the light reaction complex are plastocyanin, ferredoxin [2Fe-2S], chlorophyll A-B binding protein, photosystem II protein PsbX, photosystem II protein PsbW, photosystem II protein PsbY, photosystem II oxygen evolving complex protein PsbP, photosystem II protein PsbR, photosystem II manganese-stabilizing protein PsbO, photosystem II oxygen evolving complex protein PsbQ, photosystem I reaction centre (subunit XI PsaL), photosystem I psaG/psaK protein, photosystem I reaction centre subunit N, photosystem I reaction center protein PsaF (subunit III), NADH:flavin oxidoreductase/NADH oxidase, and cytochrome b ubiquinol oxidase. The ratios of up- (+) or down (-) -regulated tags are indicated. Detailed information for light reaction complexes is listed in Additional file . Note that the key enzymes are either up- or down-regulated in three tissues; this behavior suggests active yet unique regulations in the hybrid

How many human genes can be defined as housekeeping with current expression data?-3

compared among total genes and HK genes defined in 18 tissues. The expression breadth distribution of total genes in 51 tissues has two modes representing TS and HK genes respectively, but due to the limited gene detectability in poorly sampled tissues, the spike of HK genes peaks at value 35 and diminishes as tissue broadness increases. The expression breadths of HK genes defined in 18 tissues peak at about value 42 showing very broad expression in 51 tissues.<p><b>Copyright information:</b></p><p>Taken from "How many human genes can be defined as housekeeping with current expression data?"</p><p>http://www.biomedcentral.com/1471-2164/9/172</p><p>BMC Genomics 2008;9():172-172.</p><p>Published online 16 Apr 2008</p><p>PMCID:PMC2396180.</p><p></p

How many human genes can be defined as housekeeping with current expression data?-0

Ata (A). Tissues are ranked from the poorly-sampled (left) to the highly-sampled (right) according to the EST data. The numbers of detected genes are plotted against the numbers of sampled ESTs for the 18 tissues (B). The sampling growth curve is fitted by Hill function () = /() with = 17622.8, = 0.8, = 6259.7. The curve indicates that current transcriptome sampling is far from saturated. Percentage of genes is plotted against the number of tissues where they express to give the expression breadth distribution (C). Expression breadth in microarray data is compared against that in EST data, with color from white to blue indicating the number of incidence from low to high (D). The correlation of expression breadths between the two types of data is not significant (= 0.42); 71% of the genes are detected in less number of tissues by microarray data than by EST data.<p><b>Copyright information:</b></p><p>Taken from "How many human genes can be defined as housekeeping with current expression data?"</p><p>http://www.biomedcentral.com/1471-2164/9/172</p><p>BMC Genomics 2008;9():172-172.</p><p>Published online 16 Apr 2008</p><p>PMCID:PMC2396180.</p><p></p

Differential gene expression in an elite hybrid rice cultivar () and its parental lines based on SAGE data-0

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in an elite hybrid rice cultivar () and its parental lines based on SAGE data"</p><p>http://www.biomedcentral.com/1471-2229/7/49</p><p>BMC Plant Biology 2007;7():49-49.</p><p>Published online 19 Sep 2007</p><p>PMCID:PMC2077334.</p><p></p>A, UniGene, and ST; see Materials and Methods) were used for the construction of virtual transcripts. When the transcript sequences extend beyond the predicated coding sequence were available, the UTR sequences were aligned and determined (A). When the information was not available, the theoretical 3' UTR sequences were determined based on a stepwise (100-, 200-, 300-, 400-, and 500 bp) assessment of the genome sequences and added after the stop codons (B). Nearly 58.7% of the assigned tags have a 3'-UTR length of 300 bp

Transcriptome-wide N⁶-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification

<div><p><i>N</i>⁶-methyladenosine (m⁶A) is the most prevalent internal modification present in mRNAs of all higher eukaryotes. With the development of MeRIP-seq technique, in-depth identification of mRNAs with m⁶A modification becomes feasible. Here we present a transcriptome-wide m⁶A modification profiling effort for rice transcriptomes of differentiated callus and leaf, which yields 8,138 and 14,253 m⁶A-modified genes, respectively. The m⁶A peak (m⁶A-modified nucleotide position on mRNAs) distribution exhibits preference toward both translation termination and initiation sites. The m⁶A peak enrichment is negatively correlated with gene expression and weakly positively correlated with certain gene features, such as exon length and number. By comparing m⁶A-modified genes between the 2 samples, we define 1,792 and 6,508 tissue-specific m⁶A-modified genes (TSMGs) in callus and leaf, respectively. Among which, 626 and 5,509 TSMGs are actively expressed in both tissues but are <u>s</u>electively m⁶A-<u>m</u>odified (SMGs) only in one of the 2 tissues. Further analyses reveal characteristics of SMGs: (1) Most SMGs are differentially expressed between callus and leaf. (2) Two conserved RNA-binding motifs, predicted to be recognized by PUM and RNP4F, are significantly over-represented in SMGs. (3) GO enrichment analysis shows that SMGs in callus mainly participate in transcription regulator/factor activity whereas SMGs in leaf are mainly involved in plastid and thylakoid. Our results suggest the presence of tissue-specific competitors involved in SMGs. These findings provide a resource for plant RNA epitranscriptomic studies and further enlarge our knowledge on the function of RNA m⁶A modification.</p></div

Mechanism Analysis of Acid Tolerance Response of <em>Bifidobacterium longum</em> subsp. <em>longum</em> BBMN 68 by Gene Expression Profile Using RNA-Sequencing

<div><p>To analyze the mechanism of the acid tolerance response (ATR) in <em>Bifidobacterium longum</em> subsp. <em>longum</em> BBMN68, we optimized the acid-adaptation condition to stimulate ATR effectively and analyzed the change of gene expression profile after acid-adaptation using high-throughput RNA-Seq. After acid-adaptation at pH 4.5 for 2 hours, the survival rate of BBMN68 at lethal pH 3.5 for 120 min was increased by 70 fold and the expression of 293 genes were upregulated by more than 2 fold, and 245 genes were downregulated by more than 2 fold. Gene expression profiling of ATR in BBMN68 suggested that, when the bacteria faced acid stress, the cells strengthened the integrity of cell wall and changed the permeability of membrane to keep the H⁺ from entering. Once the H⁺ entered the cytoplasm, the cells showed four main responses: First, the F₀F₁-ATPase system was initiated to discharge H⁺. Second, the ability to produce NH₃ by cysteine-cystathionine-cycle was strengthened to neutralize excess H⁺. Third, the cells started NER-UVR and NER-VSR systems to minimize the damage to DNA and upregulated HtpX, IbpA, and γ-glutamylcysteine production to protect proteins against damage. Fourth, the cells initiated global response signals ((p)ppGpp, polyP, and Sec-SRP) to bring the whole cell into a state of response to the stress. The cells also secreted the quorum sensing signal (AI-2) to communicate between intraspecies cells by the cellular signal system, such as two-component systems, to improve the overall survival rate. Besides, the cells varied the pathways of producing energy by shifting to BCAA metabolism and enhanced the ability to utilize sugar to supply sufficient energy for the operation of the mechanism mentioned above. Based on these reults, it was inferred that, during industrial applications, the acid resistance of bifidobacteria could be improved by adding BCAA, γ-glutamylcysteine, cysteine, and cystathionine into the acid-stress environment.</p> </div

Effects of acid- adaptation on acid resistance of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BBMN68.

<p>Control cells were not treated; acid-adaptation cells were acid-adapted at pH 4.5 for 2 hours; acid resistance shows the survival ratios of the cells at pH 3.5 for 2 hours. * significant difference (<i>P</i><0.05).</p

Expression of genes encoding molecular chaperones in BBMN68.

*<p>changed by more than 2 fold.</p