BIAS: Bioinformatics Integrated Application Software

Finak, Greg; Godin, Noa; Hallett, Michael; Pépin, François; Rajabi, Z.; Srivastava, Varun; Tang, Zuojian

doi:10.1093/bioinformatics/bti170

Cited by 10 publications

(8 citation statements)

References 1 publication

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“…15). Data preprocessing and normalization were automated using the BIAS system (16). Raw feature intensities were background corrected using the RMA background correction algorithm (17).…”

Section: Methodsmentioning

confidence: 99%

Distinct ErbB-2–Coupled Signaling Pathways Promote Mammary Tumors with Unique Pathologic and Transcriptional Profiles

et al. 2007

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ErbB-2 overexpression and amplification occurs in 15% to 30% of human invasive breast carcinomas associated with poor clinical prognosis. Previously, we have shown that four ErbB-2/Neu tyrosine-autophosphorylation sites within the cytoplasmic tail of the receptor recruit distinct adaptor proteins and are sufficient to mediate transforming signals in vitro. Two of these sites, representing the growth factor receptor binding protein 2 (Grb2; Neu-YB) and the Src homology and collagen (Shc; Neu-YD) binding sites, can induce mammary tumorigenesis and metastasis. Here, we show that transgenic mice bearing the two other ErbB-2 autophosphorylation sites (Neu-YC and Neu-YE) develop metastatic mammary tumors. A detailed comparison of biological profiles among all Neu mutant mouse models revealed that Neu-YC, Neu-YD, and Neu-YE mammary tumors shared similar pathologic and transcriptional features. By contrast, the Neu-YB mouse model displayed a unique pathology with a high metastatic potential that correlates with a distinct transcriptional profile, including genes that promote malignant tumor progression such as metalloproteinases and chemokines. Furthermore, Neu-YB tumor epithelial cells showed abundant intracellular protein level of the chemokine CXCL12/SDF-1A, which may reflect the aggressive nature of this Neu mutant mouse model. Taken together, these findings indicate that activation of distinct Neu-coupled signaling pathways has an important impact on the biological behavior of Neu-induced tumors. [Cancer Res 2007;67(16):7579-88]

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“…15). Data preprocessing and normalization were automated using the BIAS system (16). Raw feature intensities were background corrected using the RMA background correction algorithm (17).…”

Section: Methodsmentioning

confidence: 99%

Distinct ErbB-2–Coupled Signaling Pathways Promote Mammary Tumors with Unique Pathologic and Transcriptional Profiles

et al. 2007

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“…Outlier features on the arrays were flagged by the same software package. Data preprocessing and normalization was automated using the BIAS system (50). Raw feature intensities were background corrected using the RMA background correction algorithm (51,52), and the resulting expression estimates were converted to log 2 ratios.…”

Section: Gene Expression Analysismentioning

confidence: 99%

Osteoactivin Promotes Breast Cancer Metastasis to Bone

Rose

Pépin

Russo

et al. 2007

Molecular Cancer Research

149

159

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The skeleton is a preferred site of metastasis in patients with disseminated breast cancer. We have used 4T1 mouse mammary carcinoma cells, which metastasize to bone from the mammary fat pads of immunocompetent mice, to identify novel genes involved in this process. In vivo selection of parental cells resulted in the isolation of independent, aggressively bone metastatic breast cancer populations with reduced metastasis to the lung. Gene expression profiling identified osteoactivin as a candidate that is highly and selectively expressed in aggressively bone metastatic breast cancer cells. These cells displayed enhanced migratory and invasive characteristics in vitro, the latter requiring sustained osteoactivin expression. Osteoactivin depletion in these cells, by small interfering RNA, also lead to a loss of matrix metalloproteinase-3 expression, whereas forced osteoactivin expression in parental 4T1 cells was sufficient to elevate matrix metalloproteinase-3 levels, suggesting that this matrix metalloproteinase may be an important mediator of osteoactivin function. Overexpression of osteoactivin in an independent, weakly bone metastatic breast cancer cell model significantly enhanced the formation of osteolytic bone metastases in vivo. Finally, high levels of osteoactivin expression in primary human breast cancers correlate with estrogen receptor -negative status and increasing tumor grade. Thus, we have identified osteoactivin as a protein that is expressed in aggressive human breast cancers and is capable of promoting breast cancer metastasis to bone.

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“…Python scripts are also provided as examples of how to implement this concept without the need of any SQL or programming knowledge and how to integrate RDBMS with analysis packages (like EMBOSS). Several complete software packages with relational database backend appeared recently [38][39][40], but none could be easily applied to our project. Some of them are gene-centric (e.g.…”

Section: Discussionmentioning

confidence: 99%

Search for proteins with similarity to the CFTR R domain using an optimized RDBMS solution, mBioSQL

Hegedüs

Riordan

2006

Open Life Sciences

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Abstract:The cystic fibrosis transmembrane conductance regulator (CFTR) comprises ATP binding and transmembrane domains, and a unique regulatory (R) domain not found in other ATP binding cassette proteins. Phosphorylation of the R domain at different sites by PKA and PKC is obligatory for the chloride channel function of CFTR. Sequence similarity searches on the R domain were uninformative. Furthermore, R domains from different species show low sequence similarity. Since these R domains resemble each other only in the location of the phosphorylation sites, we generated different R domain patterns masking amino acids between these sites. Because of the high number of the generated patterns we expected a large number of matches from the UniProt database. Therefore, a relational database management system (RDBMS) was set up to handle the results. During the software development our system grew into a general package which we term Modular BioSQL (mBioSQL). It has higher performance than other solutions and presents a generalized method for the storage of biological result-sets in RDBMS allowing convenient further analysis. Application of this approach revealed that the R domain phosphorylation pattern is most similar to those in nuclear proteins, including transcription and splicing factors.

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BIAS: Bioinformatics Integrated Application Software

Abstract: hallett@mcb.mcgill.ca.

Cited by 10 publications

References 1 publication

Distinct ErbB-2–Coupled Signaling Pathways Promote Mammary Tumors with Unique Pathologic and Transcriptional Profiles

Distinct ErbB-2–Coupled Signaling Pathways Promote Mammary Tumors with Unique Pathologic and Transcriptional Profiles

Osteoactivin Promotes Breast Cancer Metastasis to Bone

Search for proteins with similarity to the CFTR R domain using an optimized RDBMS solution, mBioSQL

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