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No-match ORESTES explored as tumor markers

ABSTRACT: Sequencing technologies together with new bioinformatics tools have led to the complete sequencing of various genomes. However, information regarding the human transcriptome and its annotation is yet to be completed. The Human Cancer Genome Project, using ORESTES (open reading frame EST sequences) methodology, contributed to this major objective by generating data from about 1.2 million expressed sequence tags (ESTs). Approximately 30% of these sequences did not align to ESTs in the public databases and were considered no-match ORESTES. On the basis that a set of these ESTs could represent new transcripts, we constructed a cDNA microarray. This platform was used to hybridize against 12 different normal or tumor tissues. We identified 3,421 transcribed regions not associated with annotated transcripts, representing 83.3% of the platform. The total number of differentially expressed sequences, with fold differences between tumor and normal samples of at least two, in one or more different tissues, was 1,007. Also, about 28% of analyzed sequences could represent non-coding RNAs (ncRNAs). Our data reinforces the knowledge of the human genome being pervasively transcribed, and point out molecular marker candidates for different cancers. To reinforce our data, we confirmed, by real-time PCR, the differential expression of 3 out of 8 potentially tumor markers in prostate tissues. A list of 1,007 differentially expressed sequences, as well as the 291 potentially non-coding molecular markers for different tumors was provided.

ORGANISM(S): Homo sapiens

PROVIDER: GSE12737 | GEO | 2009/04/13

SECONDARY ACCESSION(S): PRJNA111041

REPOSITORIES: GEO

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No-match ORESTES explored as tumor markers

Project description:Sequencing technologies together with new bioinformatics tools have led to the complete sequencing of various genomes. However, information regarding the human transcriptome and its annotation is yet to be completed. The Human Cancer Genome Project, using ORESTES (open reading frame EST sequences) methodology, contributed to this major objective by generating data from about 1.2 million expressed sequence tags (ESTs). Approximately 30% of these sequences did not align to ESTs in the public databases and were considered no-match ORESTES. On the basis that a set of these ESTs could represent new transcripts, we constructed a cDNA microarray. This platform was used to hybridize against 12 different normal or tumor tissues. We identified 3,421 transcribed regions not associated with annotated transcripts, representing 83.3% of the platform. The total number of differentially expressed sequences, with fold differences between tumor and normal samples of at least two, in one or more different tissues, was 1,007. Also, about 28% of analyzed sequences could represent non-coding RNAs (ncRNAs). Our data reinforces the knowledge of the human genome being pervasively transcribed, and point out molecular marker candidates for different cancers. To reinforce our data, we confirmed, by real-time PCR, the differential expression of 3 out of 8 potentially tumor markers in prostate tissues. A list of 1,007 differentially expressed sequences, as well as the 291 potentially non-coding molecular markers for different tumors was provided. Experiments were performed in duplicate, using dye-swap method. We used linearly amplified RNA samples (T7-based protocol), derived from 56 normal or tumor tissues from 12 distincts body localization, and a pool of RNAs obtained from 15 distinct human cell lines as reference. cDNA was synthesized in the presence of aminoallyl-dUTP (Sigma-Aldrich) and labeled using Alexa Fluor 555 or Alexa Fluor 647 dyes (Invitrogen).

2009-04-13 | E-GEOD-12737 | biostudies-arrayexpress

No-match ORESTES explored as tumor markers.

Project description:Sequencing technologies and new bioinformatics tools have led to the complete sequencing of various genomes. However, information regarding the human transcriptome and its annotation is yet to be completed. The Human Cancer Genome Project, using ORESTES (open reading frame EST sequences) methodology, contributed to this objective by generating data from about 1.2 million expressed sequence tags. Approximately 30% of these sequences did not align to ESTs in the public databases and were considered no-match ORESTES. On the basis that a set of these ESTs could represent new transcripts, we constructed a cDNA microarray. This platform was used to hybridize against 12 different normal or tumor tissues. We identified 3421 transcribed regions not associated with annotated transcripts, representing 83.3% of the platform. The total number of differentially expressed sequences was 1007. Also, 28% of analyzed sequences could represent noncoding RNAs. Our data reinforces the knowledge of the human genome being pervasively transcribed, and point out molecular marker candidates for different cancers. To reinforce our data, we confirmed, by real-time PCR, the differential expression of three out of eight potentially tumor markers in prostate tissues. Lists of 1007 differentially expressed sequences, and the 291 potentially noncoding tumor markers were provided.

| S-EPMC2677862 | biostudies-literature

Identification of testis-relevant genes from testes ESTs and cDNA microarray in the black tiger shrimp

Project description:Identification of testis-relevant genes using in silico analysis from testes ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon) A total of 4,803 ESTs from the testis library were unidirectionally sequenced and analyzed in silico using a customizable data analysis package, ESTplus. A total of 2,702 unique sequences from 424 contigs and 2,278 singletons were identified. Approximately, 1,134 sequences from the total of 2,702 unique sequences (contigs and singletons) are homologous to genes with known functions. Some of which (mago nashi, insulin-degrading enzyme, actin-depolymerizing factor) are related to testicular development in studies of other organisms. Moreover, the sequences were further characterized according to the gene ontology categories (41% biological process, 24% molecular function, 35% cellular component). By comparing with the EST libraries of other tissues, a total of 1,579 possible testis-specific ESTs were identified. Some of these testis-specific ESTs, such as Phospholipase A2 and Matrix Metalloproteinases, have functions relevant to testicular development. In addition, novel ESTs (621 ESTs) that have never been identified in any ESTs from the Penaeidae family were found in this study. Through cDNA microarray analysis, some of testis-specific ESTs were preferentially expressed in testes to ovary; one of which was a saposin homolog. Therefore, saposin was further characterized by real-time PCR and its full-length sequence was obtained by RACE-PCR.

2010-11-04 | GSE19037 | GEO

Project description:Melilotus albus different tissues RNA sequences

| PRJNA647665 | ENA

Identification of testis-relevant genes from testes ESTs and cDNA microarray in the black tiger shrimp

2010-11-04 | E-GEOD-19037 | biostudies-arrayexpress

Fire ant adult vs brood comparison for microarray quality control

Project description:Ants display a range of fascinating behaviors, a remarkable level of intra-species phenotypic plasticity and many other interesting characteristics. Here we present a new tool to study the molecular mechanisms underlying these traits: a tentatively annotated expressed sequence tag (EST) resource for the fire ant Solenopsis invicta. From a normalized cDNA library we obtained 21,715 ESTs, which represent 11,864 putatively different transcripts with very diverse molecular functions. All ESTs were used to construct a cDNA microarray. We compared mixed adults to mixed brood to test the quality of the microarrays. Keywords: microarray quality control

2006-10-14 | GSE5995 | GEO

Analysis of global gene expression signatures in sweet potato as affected by temperature stress

Project description:Global gene expression signatures was analysed through microarray expression profiling as a discovery platform to identify up and down regulated ESTs that represent genes involved in metabolic pathways in the leaf, fibrous root and storage root (tuber forming root) of sweetpotato (Ipomoea batatas) as affcted by high temperature stress (40oC) compared to ambient temperature (30oC). Also Global gene expression signatures was analysed by the same procedure to explore up and down regulated ESTs in tuberous root of sweet potato in comparison with fibrous root of Ipomoea cornea and identify unique ESTs that represent genes involved in tuber formation in sweet potato.

2015-10-01 | GSE51862 | GEO

Proteomic analysis of the shell organic matrix of Spondylus Gaederopus

Project description:This work reports a comprehensive and integrated microstructural, biochemical and proteomics study on the shell matrix of Spondylus gaederopus, the Mediterranean thorny oyster. We investigate the skeletal matrix proteins which are involved in biomineralization and compare the identified Spondylus sequences with other shell proteins, that are publicly available in databases. Using high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS) we characterized several shell protein fractions, isolated by different bleaching treatments. We identified six shell proteins, which also displayed features and domains typically found in biomineralized tissues, including the prevalence of intrinsically disordered regions. However, many reconstructed peptide sequences (de novo) could not be matched to any known shell proteins and we suggest that these probably represent lineage-specific sequences. The proteomic data implies that Spondylus may have evolved a distinct molecular toolkit for biomineralization. Using high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS) we characterized several shell protein fractions, isolated by different bleaching treatments. Six shell proteins were identified, which displayed features and domains typically found in biomineralized tissues, including the prevalence of intrinsically disordered regions. However, most of the reconstructed peptide sequences (de novo) could not be matched to any known shell proteins and probably represent lineage-specific sequences.

2020-03-31 | PXD016760 | Pride

Oligoarray analysis of semi-global gene expression in ripening Japanese pear fruit

Project description:A custom oligoarray of Japanese pear (Pyrus pyrifolia) based on 9,812 independent ESTs from different tissues (fruits at various growth stages, vegetative and flower tissues) was designed and used for comprehensive investigation of gene expression before and during ripening (105 to 147 days after full bloom).

2010-10-12 | GSE18682 | GEO

Analysis of a normalised equine cDNA library using deep sequencing

Project description:While a first draft of the equine genome is available and predictions are made regarding resulting genes and proteins, little is known about the actual transcriptome. So far, published expressed sequence tags (ESTs) from different horse tissues were generally rather short (≤600bp) and hardly annotated, reflecting the problem that good cDNA libraries are very difficult to analyse. In this approach, we aimed to establish and analyse a normalised immune cell cDNA library (using freshly isolated and activated lymphocytes, NK cells, monocytes and DC). In particular, we wanted to test next generation sequencing combined with a series of bioinformatic approaches. The resulting cDNA library contained 2x107 clones of which 1056 were used for an initial Sanger sequencing and 4x106 for the deep sequencing analysis. Through the latter we obtained >29k sequences for which more than 5000 matches where found on the equine reference sequences. Additionally we could identify more than 3500 sequences which had matches on both - non-equine RNA sequences as well as the equine genome. In these we find both extensions of existing RefSeq models and novel mRNAs alike. Less than 2% of sequences did not have any match in the mentioned databases.

2012-06-30 | GSE26794 | GEO

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