Novel Human Leukocyte Interferon Subtype and Structural Comparison of Alpha Interferon Genes

Gren, E.J.; Berzin, V.; Jansone, Inta; Tsimanis, A. Yu.; Vishnevsky, Y.; Apsalons, U.

doi:10.1089/jir.1984.4.609

Cited by 18 publications

(2 citation statements)

References 31 publications

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“…On the p arm of chromosome 9 there are 13 closely related genes for interferon alphas (23). There are 13 probesets on the U133 plus 2.0 chip that detect these genes.…”

Section: Resultsmentioning

confidence: 99%

A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array

Harbig

Sprinkle

Enkemann

2005

Nucleic Acids Research

115

102

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One of the biggest problems facing microarray experiments is the difficulty of translating results into other microarray formats or comparing microarray results to other biochemical methods. We believe that this is largely the result of poor gene identification. We re-identified the probesets on the Affymetrix U133 plus 2.0 GeneChip array. This identification was based on the sequence of the probes and the sequence of the human genome. Using the BLAST program, we matched probes with documented and postulated human transcripts. This resulted in the redefinition of approximately 37% of the probes on the U133 plus 2.0 array. This updated identification specifically points out where the identification is complicated by cross-hybridization from splice variants or closely related genes. More than 5000 probesets detect multiple transcripts and therefore the exact protein affected cannot be readily concluded from the performance of one probeset alone. This makes naming difficult and impacts any downstream analysis such as associating gene ontologies, mapping affected pathways or simply validating expression changes. We have now automated the sequence-based identification and can more appropriately annotate any array where the sequence on each spot is known.

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“…On the p arm of chromosome 9 there are 13 closely related genes for interferon alphas (23). There are 13 probesets on the U133 plus 2.0 chip that detect these genes.…”

Section: Resultsmentioning

confidence: 99%

A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array

Harbig

Sprinkle

Enkemann

2005

Nucleic Acids Research

115

102

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“…The complexity of the gene families encoding aand 3-interferons has been revealed using a combination of gene cloning and DNA hybridizatlon techniques (2). In humans, the IFN-a class consists of at least 13 members whlch are more than 77X homologous in amino acid sequence (3)(4)(5)(6)(7)(8)(9).…”

Section: Introductionmentioning

confidence: 99%

A novel class of human type I interferons

Hauptmann¹,

Swetly²

1985

Nucl Acids Res

100

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The screening of a cDNA library prepared from mRNA of Sendai virus induced Namalwa (human Burkitt's lymphoma) cells, using a human IFN-alpha 2 DNA probe under conditions of low stringency, identified two weakly hybridizing clones containing sequences related to, but discernably different from those of the IFN-alpha class. Sequence and hybridization analysis of these cDNAs as well as expression in E. coli provided evidence that they encode proteins which have the characteristics of IFN type I but which are sufficiently diverged in sequence from both IFN-alpha s and IFN-beta to suggest that they are representatives of a new and distinct class of interferons named interferon-omega. Hybridization of these sequences to genomic DNA reveals that this class contains at least four members.

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A few distinct ?molecular sandwiches? are basis for structural and functional similarities of subspecies of interferon ? and of families of growth-promoting hormones

et al. 1986

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'Molecular sandwiches' composed of two aromatic amino acids separated by a hydrophilic one were found on eleven subspecies of human interferon alpha, on murine interferon alpha 2, and human interferon beta 1. In addition, another type of the sandwiches was found on several species of interferon. This confirms and extends the observations concerning the similarities between some interferons and several classical hormones. Furthermore, we are presenting evidence that a distinct type of the 'molecular sandwiches': Tyr-Cys...Cys and/or Cys...Cys-Cys...Cys, that participate in formation of disulfide bonds, is a characteristic marker of most, if not all of the growth-promoting hormones including growth factors. The 'sandwiches' appear to be important for receptor binding.

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Novel Human Leukocyte Interferon Subtype and Structural Comparison of Alpha Interferon Genes

Cited by 18 publications

References 31 publications

A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array

A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array

A novel class of human type I interferons

A few distinct ?molecular sandwiches? are basis for structural and functional similarities of subspecies of interferon ? and of families of growth-promoting hormones

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