Project description:A collection of 237,000 expressed sequence tags generated by the Sugarcane EST sequencing project (SUCEST) was analyzed in search of signal transduction components. The SUCAST (Sugarcane Signal Transduction) Catalogue contains over 3500 components, with around 2900 involved in several aspects of cell signaling and transcription. Sequence comparisons and conserved protein domain analysis revealed 477 receptors, 510 protein kinases, 107 protein phosphatases, a large number of small GTPases, G-proteins, members of the calcium and inositol metabolism, and other signal transduction-related proteins. Over 600 transcription factors were also indexed. Moreover, 437 genes with no matches in the public databases and 111 genes of unknown function were catalogued. Several of the SUCEST cDNA libraries were derived from plants submitted to abiotic stresses or infected with endophytic nitrogen fixing bacteria and stress and pathogen response-related genes were also annotated. The abundance of transcripts among six different sugarcane tissues (flowers, roots, leaves, lateral buds, 1st and 4th internodes) was evaluated using microarrays and expression profile clustering. We identified 216 genes that are significantly more abundant in one of the tissues analyzed. A subset of the data was validated by real-time PCR. Additionally, genes with similar expression levels among different tissues were identified. The characterization of these elements and their promoters can aid in the development of tools for the genetic manipulation of this plant species and other economically important grasses. Keywords: other

2005-08-24 | GSE1702 | GEO

The Unified Human Gastrointestinal Genome catalogue

Project description:A unified sequence catalogue of the human gut microbiome

| PRJEB33885 | ENA

Catalogue of genomic alterations in uterine cervical carcinoma of Indian patients.

Project description:To identify genomic alterations in uterine cervical carcinoma of Indian patients. Cancer of the uterine cervix (CACX) is the fourth most frequent carcinoma among women worldwide. In India, it accounts for approximately 132,000 new cases and 74,000 deaths annually contributing to nearly 1/3rd of the global cervical cancer deaths. Although, several etiological factors such as use of oral contraceptives, precocious marriage, multiparity, smoking etc. are seen to modify the risk of CACX, but infection by high risk human papillomavirus (hrHPV) is thought to be the major cause. Interestingly, long latency period for malignant outcome in only a subset of HPV-infected women indicates involvement of additional chromosomal alterations.Since the first report of changes in chromosomal content of CACX, several genome-wide studies reported frequent chromosomal gain of 3q (3q24–29), 1q (1q22–q23, 1q25.3–q32.1) and 5p (5p12–p13) and loss of 3p (3p12–23), 11q (11q22.3–25) and 4p (4p16.3–p16.1). But no study was done to catalogue the precise genomic alterations in CACX of Indian patients. To the best of our knowledge, for the first time the present study revealed precise chromosomal aberrations with differential frequency in Indian CACX patients (n=11). Among these alterations, frequent (>50%) amplifications of distinct chromosomal loci were as follows: 1p36.11-1p31.1, 1q21.1-1q44, 3q13.13-3q29, 5p15.33-5p12, 8q24.3, 16q22.2, 19q13.13-19q13.2, Xp22.33-Xp11.21 and Xq11.2-Xq12. While recurrent (>35%) loss at chromosomal loci, 2q34-2q37.3, 4p16.3-4p12, 4q21.3, 8p23.3, 8p23.2, 8p11.22, 11q14.1-11q25, 13q13.3-13q14.3, and 19p13.3 were also observed. All CACX patients showed precise amplification of chromosome 3 at coordinates 3q25.2-3q26.1 (chr3:154427429-162796745), 3q26.1-3q26.31 (chr3:162901354-175146595) and 3q26.32-3q29 (chr3:175208719-198094926). Highest (72%) loss of chromosomal loci 11q24.3-11q25 (chr11:128926744-135034169) was seen.

2016-12-27 | GSE76911 | GEO

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