GeneCards/spl trade/ 2002: an evolving human gene compendium

Solomon, I.; Shmueli, Orit; Lapidot, Michal; Shen-Orr, Shai S.; Adato, Avital; Ben-Dor, Uri; Esterman, Nir; Rosen, Naomi; Peter, Inga; Olender, Tsviya; Chalifa-Caspi, Vered; Lancet, Doron

doi:10.1109/csb.2002.1039362

Cited by 3 publications

(3 citation statements)

References 2 publications

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“…Most interestingly, the probe 326_i_at appears in conjunction with the ribosome pathway amongst high- S GPC pairs. In fact, 326_i_at is a probe for the ribosomal protein RPS20 [ 30 ] (and hence is part of the ribosome pathway); the absence of this annotation in the Bioconductor HGU95AV2 package permitted its inclusion despite the fact that it fails the g ∉ G P criterion. As a result, the 326_i_at was treated by the analysis as if it were not part of the ribosome pathway, yet it was clearly identified as a gene of interest with respect to the ribosome pathway, for which the expressions are correlated in normal and adenocarcinoma samples but not in squamous cell carcinoma.…”

Section: Resultsmentioning

confidence: 99%

Identifying differential correlation in gene/pathway combinations

2008

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Background: An important emerging trend in the analysis of microarray data is to incorporate known pathway information a priori. Expression level "summaries" for pathways, obtained from the expression data for the genes constituting the pathway, permit the inclusion of pathway information, reduce the high dimensionality of microarray data, and have the power to elucidate gene-interaction dependencies which are not already accounted for through known pathway identification.

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Section: Resultsmentioning

confidence: 99%

Identifying differential correlation in gene/pathway combinations

2008

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“…This database compiles information on mRNA expression in a total of 23 different normal human tissues hybridized against the Affymetrix HG-U95A-E and HG-U133A DNA-microarrays, respectively. 32 The results are presented in the Supporting Information (Figure S1), indicating that SPRL1 has probably an important physiological role. To this end, literature shows that SPRL1 is expressed on the basal, lateral, and apical surfaces of endothelial cells but not at the basement membrane.…”

Section: ■ Discussionmentioning

confidence: 99%

Sparc-Like Protein 1 Is a New Marker of Human Glioma Progression

et al. 2012

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High-grade gliomas (glioblastomas) are the most common and deadly brain tumors in adults, currently with no satisfactory treatment available. Apart from de novo glioblastoma, it is currently accepted that these malignancies mainly progress from lower grade glial tumors. However, the molecular entities governing the progression of gliomas are poorly understood. Extracellular and membrane proteins are key biomolecules found at the cell-to-cell communication interface and hence are a promising proteome subpopulation that could help understand the development of glioma. Accordingly, the current study aims at identifying new protein markers of human glioma progression. For this purpose, we used glial tumors generated orthotopically with T98G and U373 human glioma cells in nude mice. This setup allowed also to discriminate the protein origin, namely, human (tumor) or mouse (host). Extracellular and membrane proteins were selectively purified using biotinylation followed by streptavidin affinity chromatography. Isolated proteins were digested and then identified and quantified employing 2D-nano-HPLC−MS/MS analysis. A total of 23 and 27 upregulated extracellular and membrane proteins were identified in the T98G and U373 models, respectively. Approximately two-thirds of these were predominantly produced by the tumor, whereas the remaining proteins appeared to be mainly overexpressed by the host tissue. Following extensive validation, we have focused our attention on sparc-like protein 1. This protein was further investigated using immunohistochemistry in a large collection of human glioma samples of different grades. The results showed that sparc-like protein 1 expression correlates with glioma grade, suggesting the possible role for this protein in the progression of this malignancy.

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“…Ankyrin repeat domain 30A (ANKRD30A) encodes a transcription factor that is exclusively expressed in the breast and the testis. Deregulated expression levels have been correlated with breast cancer progression [59].…”

Section: Discussionmentioning

confidence: 99%

Portrait of Tissue-Specific Coexpression Networks of Noncoding RNAs (miRNA and lncRNA) and mRNAs in Normal Tissues

Cava

Bertoli

Castiglioni

2019

Computational and Mathematical Methods in Medicine

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Genes that encode proteins playing a role in more than one biological process are frequently dependent on their tissue context, and human diseases result from the altered interplay of tissue- and cell-specific processes. In this work, we performed a computational approach that identifies tissue-specific co-expression networks by integrating miRNAs, long-non-coding RNAs, and mRNAs in more than eight thousands of human samples from thirty normal tissue types. Our analysis (1) shows that long-non coding RNAs and miRNAs have a high specificity, (2) confirms several known tissue-specific RNAs, and (3) identifies new tissue-specific co-expressed RNAs that are currently still not described in the literature. Some of these RNAs interact with known tissue-specific RNAs or are crucial in key cancer functions, suggesting that they are implicated in tissue specification or cell differentiation.

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GeneCards/spl trade/ 2002: an evolving human gene compendium

Cited by 3 publications

References 2 publications

Identifying differential correlation in gene/pathway combinations

Identifying differential correlation in gene/pathway combinations

Sparc-Like Protein 1 Is a New Marker of Human Glioma Progression

Portrait of Tissue-Specific Coexpression Networks of Noncoding RNAs (miRNA and lncRNA) and mRNAs in Normal Tissues

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