Journal: BMC Bioinformatics

Article Title: Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method

doi: 10.1186/1471-2105-9-508

Figure Lengend Snippet: Preferential correlation changes between gene pairs . RSPR-NR was applied to the Arabidopsis expression profile data set. The cosine correlations between each of 80,000 randomly sampled gene pairs before and after RSPR-NR were recorded. The angle corresponding to each cosine correlation value was used in the plots. (A) The angle change from before RSPR-NR to after RSPR-NR is plotted along the angle before RSPR-NR, for the sampled gene pairs. A loess fit curve for the distribution is shown in gray. (B) From (A), the loess fit curve values were made zero (gray line) to normalize the distribution in small ranges of the angle before. The angle change value after this loess-based normalization is called the relative angle change value. This relative-angle-change-vs.-angle-before plot is used in (C) and (D). (C) The gene pairs that share GO process and component terms (Jaccard similarity = 0.5) are plotted. (D) The gene pairs that do not share any GO process and component terms and that have more than 5 GO terms in union among the sampled gene pairs are plotted. In both (C) and (D), the gene pairs with low correlation before RSPR-NR (an angle range between 0.3π and 0.7π) are excluded. The parameters used for RSPR-NR were a subset row number of 200, a repeat number of 20, and an FDR of 0.0316. The dot sizes in the plots were adjusted according to the density of dots in each plot.

Article Snippet: We applied the method to Arabidopsis Affymetrix microarray expression profile data collected in multiple experiments.

Techniques: Expressing

Journal: BMC Bioinformatics

Article Title: Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method

doi: 10.1186/1471-2105-9-508

Figure Lengend Snippet: Variance associated with each PC in PCA with the Arabidopsis expression profile data set . (A) The variance associated with each PC (PC1 to PC60) is plotted. (B) A close up view of (A) in the range starting with PC4.

Article Snippet: We applied the method to Arabidopsis Affymetrix microarray expression profile data collected in multiple experiments.

Techniques: Expressing

Journal: PLoS ONE

Article Title: Genome-Wide Identification and Analysis of MAPK and MAPKK Gene Families in Brachypodium distachyon

doi: 10.1371/journal.pone.0046744

Figure Lengend Snippet: Nomenclature for MAPKs and MAPKKs in Arabidopsis , Brachypodium and Oryza.

Article Snippet: Affymetrix Arabidopsis and rice microarray data were downloaded from ArrayExpress , PLEXdb and Rice Oligonucleotide Databases .

Techniques:

Journal: PLoS ONE

Article Title: Genome-Wide Identification and Analysis of MAPK and MAPKK Gene Families in Brachypodium distachyon

doi: 10.1371/journal.pone.0046744

Figure Lengend Snippet: (a) Phylogenetic relationships of B. distachyon , Arabidopsis and rice MAPK genes. The phylogenetic tree was constructed by NJ (Neighbor-joining) method using the MEGA 4 program. Different color patternings indicate different gene clusters or superclusters. (b) Comparison of CD domain among four BdMAPKs (c) Schematic diagram of amino acid motifs of B. distachyon MAPKs from different groups. Motif analysis was performed using MEME 4.0 software as described in the methods. The black solid line represents the corresponding BdMAPK and its length. The different-colored boxes represent different motifs and their position in each BdMAPK sequence. A detailed motif introduction for all the B. distachyon MAPKs is shown in .

Article Snippet: Affymetrix Arabidopsis and rice microarray data were downloaded from ArrayExpress , PLEXdb and Rice Oligonucleotide Databases .

Techniques: Construct, Software, Sequencing

Journal: PLoS ONE

Article Title: Genome-Wide Identification and Analysis of MAPK and MAPKK Gene Families in Brachypodium distachyon

doi: 10.1371/journal.pone.0046744

Figure Lengend Snippet: (a) Phylogenetic relationships of B. distachyon , Arabidopsis and rice MAPKK genes. The phylogenetic tree was constructed by NJ (Neighbor–joining) method using the MEGA 4 program. Different color patternings indicate different gene clusters or superclusters. (b) Schematic diagram of amino acid motifs of B. distachyon MAPKKs. The black solid line represents the corresponding BdMAPKK and its length. The different-colored boxes represent different motifs and their position in each BdMAPKK sequence.

Article Snippet: Affymetrix Arabidopsis and rice microarray data were downloaded from ArrayExpress , PLEXdb and Rice Oligonucleotide Databases .

Techniques: Construct, Sequencing

Journal: PLoS ONE

Article Title: Genome-Wide Identification and Analysis of MAPK and MAPKK Gene Families in Brachypodium distachyon

doi: 10.1371/journal.pone.0046744

Figure Lengend Snippet: To identify the species of origin for each chromosome, a species acronym is included before the chromosome name: At, Arabidopsis thaliana ; Os, Oryza sativa ; Bd, B.distachyon . Different color bars connect syntenic regions between B. distachyon and the other two plant species of Arabidopsis and rice chromosomes. The region of B. distachyon tightly linked cluster likely to be syntenic with that of the rice tightly linked cluster by translocation, insertion or other events was indicated with the ellipse in the same color.

Article Snippet: Affymetrix Arabidopsis and rice microarray data were downloaded from ArrayExpress , PLEXdb and Rice Oligonucleotide Databases .

Techniques: Translocation Assay

Journal: BioMed Research International

Article Title: Tools and Databases of the KOMICS Web Portal for Preprocessing, Mining, and Dissemination of Metabolomics Data

doi: 10.1155/2014/194812

Figure Lengend Snippet: The tools and databases available at KOMICS (as of November 2013).

Article Snippet: ARTRA , Database of probe information of Arabidopsis DNA microarray data (developed by Takara Bio Inc.). , http://artra.kazusa.or.jp/artra/ARI3_101/ , [ ] .

Techniques: Transgenic Assay, Microarray

Journal: STAR Protocols

Article Title: Gene coexpression analysis in Arabidopsis thaliana based on public microarray data

doi: 10.1016/j.xpro.2022.101208

Figure Lengend Snippet: Selected fields of the metadata of the samples of series E-ATMX-31

Article Snippet: The protocol below describes the specific steps for performing gene coexpression analysis on Arabidopsis thaliana Affymetrix microarray data.

Techniques: Cell Culture

Journal: STAR Protocols

Article Title: Gene coexpression analysis in Arabidopsis thaliana based on public microarray data

doi: 10.1016/j.xpro.2022.101208

Figure Lengend Snippet: Selected fields of the metadata of the samples of series E-ATMX-20

Article Snippet: The protocol below describes the specific steps for performing gene coexpression analysis on Arabidopsis thaliana Affymetrix microarray data.

Techniques:

Journal: STAR Protocols

Article Title: Gene coexpression analysis in Arabidopsis thaliana based on public microarray data

doi: 10.1016/j.xpro.2022.101208

Figure Lengend Snippet: Selected fields of the metadata of the samples of series E-GEOD-50526

Article Snippet: The protocol below describes the specific steps for performing gene coexpression analysis on Arabidopsis thaliana Affymetrix microarray data.

Techniques:

Journal: STAR Protocols

Article Title: Gene coexpression analysis in Arabidopsis thaliana based on public microarray data

doi: 10.1016/j.xpro.2022.101208

Figure Lengend Snippet: Arabidopsis thaliana gene coexpression trees as viewed by Dendroscope (A and B) Node labels are the AGI codes of the Arabidopsis thaliana genes. (A) Coexpression tree containing all Arabidopsis thaliana genes. The leaves highlighted in red denote the region where CTL2 ( AT3G16920 ) coexpression subtree is located (B) Gene coexpression subtree containing CTL2 and its coexpressed genes.

Article Snippet: The protocol below describes the specific steps for performing gene coexpression analysis on Arabidopsis thaliana Affymetrix microarray data.

Techniques:

Journal: STAR Protocols

Article Title: Gene coexpression analysis in Arabidopsis thaliana based on public microarray data

doi: 10.1016/j.xpro.2022.101208

Figure Lengend Snippet:

Article Snippet: The protocol below describes the specific steps for performing gene coexpression analysis on Arabidopsis thaliana Affymetrix microarray data.

Techniques: Microarray, Software, Western Blot