The transcriptional landscape of the mammalian genome.

This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

Protein-protein interaction panel using mouse full-length cDNAs.

We have developed a novel assay system for systematic analysis of protein-protein interactions (PPIs) that is characteristic of a PCR-mediated rapid sample preparation and a high-throughput assay system based on the mammalian two-hybrid method. Using gene-specific primers, we successfully constructed the assay samples by two rounds of PCR with up to 3.6 kb from the first-round PCR fragments. In the assay system, we designed all the steps to be performed by adding only samples, reagents, and cells into 384-well assay plates using two types of semiautomatic multiple dispensers. The system enabled us examine more than 20,000 assay wells per day. We detected 145 interactions in our pilot study using 3500 samples derived from mouse full-length enriched cDNAs. Analysis of the interaction data showed both several significant interaction clusters and predicted functions of a few uncharacterized proteins. In combination with our comprehensive mouse full-length cDNA clone bank covering a large part of the whole genes, our high-throughput assay system will discover many interactions to facilitate understanding of the function of uncharacterized proteins and the molecular mechanism of crucial biological processes, and also enable completion of a rough draft of the entire PPI panel in certain cell types or tissues of mouse within a short time.

Preprocessing implementation for microarray (PRIM): an efficient method for processing cDNA microarray data.

cDNA microarray technology is useful for systematically analyzing the expression profiles of thousands of genes at once. Although many useful results inferred by using this technology and a hierarchical clustering method for statistical analysis have been confirmed using other methods, there are still questions about the reproducibility of the data. We have therefore developed a data processing method that very efficiently extracts reproducible data from the result of duplicate experiments. It is designed to automatically filter the raw results obtained from cDNA microarray image-analysis software. We optimize the threshold value for filtering the data by using the product of N and R, where N is the ratio of the number of spots that passed the filtering vs. the total number of spots, and R is the correlation coefficient for results obtained in the duplicate experiments. Using this method to process mouse tissue expression profile data that contain 1,881,600 points of analysis, we obtained clustered results more reasonable than those obtained using previously reported filtering methods.

Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays.

We have systematically characterized gene expression patterns in 49 adult and embryonic mouse tissues by using cDNA microarrays with 18,816 mouse cDNAs. Cluster analysis defined sets of genes that were expressed ubiquitously or in similar groups of tissues such as digestive organs and muscle. Clustering of expression profiles was observed in embryonic brain, postnatal cerebellum, and adult olfactory bulb, reflecting similarities in neurogenesis and remodeling. Finally, clustering genes coding for known enzymes into 78 metabolic pathways revealed a surprising coordination of expression within each pathway among different tissues. On the other hand, a more detailed examination of glycolysis revealed tissue-specific differences in profiles of key regulatory enzymes. Thus, by surveying global gene expression by using microarrays with a large number of elements, we provide insights into the commonality and diversity of pathways responsible for the development and maintenance of the mammalian body plan.

Functional annotation of a full-length mouse cDNA collection.

The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.

KEGG: Kyoto Encyclopedia of Genes and Genomes.

Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways. The pathway information is also represented by the ortholog group tables summarizing orthologous and paralogous gene groups among different organisms. KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes. Each gene catalog is associated with the graphical genome map for chromosomal locations that is represented by Java applet. In addition to the data collection efforts, KEGG develops and provides various computational tools, such as for reconstructing biochemical pathways from the complete genome sequence and for predicting gene regulatory networks from the gene expression profiles. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/).

Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG.

The massively parallel hybridization technologies by DNA chips and microarrays make it possible to monitor expression patterns of the whole set of genes in a genome under various conditions. The vast amount of data generated by such technologies necessitates the development of a new database management system that integrates expression data with other molecular biology databases and various analysis tools. We report here an extension of our KEGG (Kyoto Encyclopedia of Genes and Genomes) and DBGET/LinkDB systems for analyzing gene expression data in conjunction with pathway information and genomic information. It is now possible to make use of expression data for the reconstruction of pathways from the complete genome sequences.

Reconstruction of amino acid biosynthesis pathways from the complete genome sequence.

The complete genome sequence of an organism contains information that has not been fully utilized in the current prediction methods of gene functions, which are based on piece-by-piece similarity searches of individual genes. We present here a method that utilizes a higher level information of molecular pathways to reconstruct a complete functional unit from a set of genes. Specifically, a genome-by-genome comparison is first made for identifying enzyme genes and assigning EC numbers, which is followed by the reconstruction of selected portions of the metabolic pathways by use of the reference biochemical knowledge. The completeness of the reconstructed pathway is an indicator of the correctness of the initial gene function assignment. This feature has become possible because of our efforts to computerize the current knowledge of metabolic pathways under the KEGG project. We found that the biosynthesis pathways of all 20 amino acids were completely reconstructed in Escherichia coli, Haemophilus influenzae, and Bacillus subtilis, and probably in Synechocystis and Saccharomyces cerevisiae as well, although it was necessary to assume wider substrate specificity for aspartate aminotransferases.

Two-component response regulators from Arabidopsis thaliana contain a putative DNA-binding motif.

An expression sequence tag database of higher plants was screened by in silico profile analysis for response regulators of the two-component regulatory system. Two closely related clones (ARR1 and ARR2), corresponding to one of the extracted candidates, were isolated from Arabidopsis thaliana. The two genes were comparably expressed in all tissues, and at higher levels in the roots. The amino-terminal half of their translation products was highly conserved. This is where a phosphate receiver domain with the landmark aspartate residue and a putative DNA-binding domain were located. Their carboxyl-terminal halves, although less similar to each other, included glutamine-rich and proline-rich regions characteristic of the transcriptional activation domain of eukaryotes. This architecture resembles that of typical bacterial response regulators serving as transcription factors.

Systematic Prediction of Orthologous Units of Genes in the Complete Genomes.

In order to fully make use of the vast amount of information in the complete genome sequences, we are developing a genome-scale system for predicting gene functions and cellular functions. The system makes use of the information of sequence similarity, the information of positional correlations in the genome, and the reference knowledge stored as the ortholog group tables in KEGG (Kyoto Encyclopedia of Genes and Genomes). The ortholog group table summarizes orthologous and paralogous relations among different organisms for a set of genes that are considered to form a functional unit, such as a conserved portion of the metabolic pathway or a molecular machinery for the membrane transport. At the moment, the ortholog group table is constructed for the cases where the genes are clustered in physically close positions in the genome for at least one organism. In this paper, we describe the system and the actual analysis of the complete genome of Pyrococcus horikoshii to identify ABC transporters.

Organizing and computing metabolic pathway data in terms of binary relations.

A new database system named KEGG is being organised to computerize functional aspects of genes and genomes in terms of the binary relations of interacting molecules or genes. We are currently working on the metabolic pathway database that is composed of three interconnected sections: genes, molecules, and pathways, which are also linked to a number of existing databases through our DBGET retrieval system. Here we present the basic concept of binary relations and hierarchical classifications to represent the metabolic pathway data. The database operations are then defined as an extension of the relational operations, and the path computation problem is considered as a deduction from binary relations. An example of using KEGG for the functional prediction of genomic sequences is presented.

[Psychogalvanogram and interpretation of human behavior]. / El psicodermogalvanograma y la interpretación del comportamiento humano.

The psychodermogalvanogram is a modern electrographical procedure whose main function depends upon a Wheatstone Bridge set at a constant voltage and with variations of intensity set up in direct relation to the conductivity of the skin. The spontaneous psychodermogalvanogram (SPDG) makes it possible to evaluate patients that could be either of a: a) normal reaction; b) hyporeactional; c) hyperreactional; d) disreactional or unstable. The psycholinguistic psychogalvanogram (PLPG) enables the possibility of distinguishing the different forms of behaviour: A) Normal reactions (+/- 80% of our clinical reports). The comportance of youths not hypnotizable or hypnocomplacent pacients, geriatrics, psychopatic personalities, electroepylepsies (GME), juvenile diabetics, etc. The PLPG presents the typical reactions in the positive answers (a marked increase in the biophasic or monophasic waves lengths) or the negative (a reduction in the volume of both waves lengths). The Time Reaction of Psycholinguistic factor (TRPL) varies from 70 to 110 ms. The comprehension of guestaltic questions arising and a repetition of the same shorten the TRPL. Rapid reaction of physic stress. Common to EEF there is an increased activity in the beta rythm prefontal left of the band 16 to 27 c/s and the paroxisms alpha prior to the right temporal of band 8 c/s and a duration of 3 to 5 seconds, equivalent answers to the PLPG. The cardiorespiratory rythm increase in relation to psychic stress. The Rheoencephalogram (REG) revealed an increase in the flown pulse of anterior cerebral artery of left hemisphere and the middle cerebral artery of right hemisphere. B) Abnormal reactions (+/- 11% of our clinical reports), which includes deep oligophrenics, schizophrenics, delirants and electroepilepsias (PME). The PLPG shows a dominance in the monophasic waves lengths at low variation similar to those found in arteriosclerosis. Paradoxically, the REG shows a marked reduction of the right carotic cerebral artery (genetic modification?). On the other hand the PLPG shows practically no reactional changes. C) Hyper reactives or sofronizables (+/- 9% of our clinical reports) includes those who can be hypnotized or are supersensitive. The PLPG reveals biondic cycles which are grouped in convexed arcs on the rise, reaching levels of 4 to 6 positive reaction, or in concave arcs on the decline reaching negative reactions. The TRPL is very brief, from 30 to 55 ms. The EEG shows in the left hemisphere, on the beta rithm basalis, alpha paroxysm of 8 c/s and 1 to 2 seconds duration wich are recorded in the prefrontal area. The right hemispheric recording, registers paroxysms of a large quantity in the theta rythm with a frequency of 5 to 6 cycles per second and a duration of 5 to 6 seconds which interrupted the beta band in a frequency of 14 to 17 c/s, similar to those registered during the drowsiness. The EOG shows very slow wyw movement. The ECG reduced its frequency and the electrospirogram (ESG) increased its volume. The pupils are parcial miotics...

El psicodermogalvanograma y la interpretación del comportamiento humano / [Psychogalvanogram and interpretation of human behavior]

The psychodermogalvanogram is a modern electrographical procedure whose main function depends upon a Wheatstone Bridge set at a constant voltage and with variations of intensity set up in direct relation to the conductivity of the skin. The spontaneous psychodermogalvanogram (SPDG) makes it possible to evaluate patients that could be either of a: a) normal reaction; b) hyporeactional; c) hyperreactional; d) disreactional or unstable. The psycholinguistic psychogalvanogram (PLPG) enables the possibility of distinguishing the different forms of behaviour: A) Normal reactions (+/- 80

of our clinical reports). The comportance of youths not hypnotizable or hypnocomplacent pacients, geriatrics, psychopatic personalities, electroepylepsies (GME), juvenile diabetics, etc. The PLPG presents the typical reactions in the positive answers (a marked increase in the biophasic or monophasic waves lengths) or the negative (a reduction in the volume of both waves lengths). The Time Reaction of Psycholinguistic factor (TRPL) varies from 70 to 110 ms. The comprehension of guestaltic questions arising and a repetition of the same shorten the TRPL. Rapid reaction of physic stress. Common to EEF there is an increased activity in the beta rythm prefontal left of the band 16 to 27 c/s and the paroxisms alpha prior to the right temporal of band 8 c/s and a duration of 3 to 5 seconds, equivalent answers to the PLPG. The cardiorespiratory rythm increase in relation to psychic stress. The Rheoencephalogram (REG) revealed an increase in the flown pulse of anterior cerebral artery of left hemisphere and the middle cerebral artery of right hemisphere. B) Abnormal reactions (+/- 11

of our clinical reports), which includes deep oligophrenics, schizophrenics, delirants and electroepilepsias (PME). The PLPG shows a dominance in the monophasic waves lengths at low variation similar to those found in arteriosclerosis. Paradoxically, the REG shows a marked reduction of the right carotic cerebral artery (genetic modification?). On the other hand the PLPG shows practically no reactional changes. C) Hyper reactives or sofronizables (+/- 9

of our clinical reports) includes those who can be hypnotized or are supersensitive. The PLPG reveals biondic cycles which are grouped in convexed arcs on the rise, reaching levels of 4 to 6 positive reaction, or in concave arcs on the decline reaching negative reactions. The TRPL is very brief, from 30 to 55 ms. The EEG shows in the left hemisphere, on the beta rithm basalis, alpha paroxysm of 8 c/s and 1 to 2 seconds duration wich are recorded in the prefrontal area. The right hemispheric recording, registers paroxysms of a large quantity in the theta rythm with a frequency of 5 to 6 cycles per second and a duration of 5 to 6 seconds which interrupted the beta band in a frequency of 14 to 17 c/s, similar to those registered during the drowsiness. The EOG shows very slow wyw movement. The ECG reduced its frequency and the electrospirogram (ESG) increased its volume. The pupils are parcial miotics...

El psicodermogalvanograma y la interpretación del comportamiento humano. / [Psychogalvanogram and interpretation of human behavior]

The psychodermogalvanogram is a modern electrographical procedure whose main function depends upon a Wheatstone Bridge set at a constant voltage and with variations of intensity set up in direct relation to the conductivity of the skin. The spontaneous psychodermogalvanogram (SPDG) makes it possible to evaluate patients that could be either of a: a) normal reaction; b) hyporeactional; c) hyperreactional; d) disreactional or unstable. The psycholinguistic psychogalvanogram (PLPG) enables the possibility of distinguishing the different forms of behaviour: A) Normal reactions (+/- 80

of our clinical reports). The comportance of youths not hypnotizable or hypnocomplacent pacients, geriatrics, psychopatic personalities, electroepylepsies (GME), juvenile diabetics, etc. The PLPG presents the typical reactions in the positive answers (a marked increase in the biophasic or monophasic waves lengths) or the negative (a reduction in the volume of both waves lengths). The Time Reaction of Psycholinguistic factor (TRPL) varies from 70 to 110 ms. The comprehension of guestaltic questions arising and a repetition of the same shorten the TRPL. Rapid reaction of physic stress. Common to EEF there is an increased activity in the beta rythm prefontal left of the band 16 to 27 c/s and the paroxisms alpha prior to the right temporal of band 8 c/s and a duration of 3 to 5 seconds, equivalent answers to the PLPG. The cardiorespiratory rythm increase in relation to psychic stress. The Rheoencephalogram (REG) revealed an increase in the flown pulse of anterior cerebral artery of left hemisphere and the middle cerebral artery of right hemisphere. B) Abnormal reactions (+/- 11

of our clinical reports), which includes deep oligophrenics, schizophrenics, delirants and electroepilepsias (PME). The PLPG shows a dominance in the monophasic waves lengths at low variation similar to those found in arteriosclerosis. Paradoxically, the REG shows a marked reduction of the right carotic cerebral artery (genetic modification?). On the other hand the PLPG shows practically no reactional changes. C) Hyper reactives or sofronizables (+/- 9

of our clinical reports) includes those who can be hypnotized or are supersensitive. The PLPG reveals biondic cycles which are grouped in convexed arcs on the rise, reaching levels of 4 to 6 positive reaction, or in concave arcs on the decline reaching negative reactions. The TRPL is very brief, from 30 to 55 ms. The EEG shows in the left hemisphere, on the beta rithm basalis, alpha paroxysm of 8 c/s and 1 to 2 seconds duration wich are recorded in the prefrontal area. The right hemispheric recording, registers paroxysms of a large quantity in the theta rythm with a frequency of 5 to 6 cycles per second and a duration of 5 to 6 seconds which interrupted the beta band in a frequency of 14 to 17 c/s, similar to those registered during the drowsiness. The EOG shows very slow wyw movement. The ECG reduced its frequency and the electrospirogram (ESG) increased its volume. The pupils are parcial miotics...