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SPEED: (S)ignaling (P)athway (E)nrichment using (E)xperimental (D)atasets. The project is part of PhD student summer research conducted by Jignesh Parikh from the Boston University Bioinformatics Program. And Bertram Klinger from the Group of Systems Biology of Molecular Networks. The SPEED project is hosted by the Group of Systems Biology of Molecular Network. At the Laboratory of Molecular Tumor Pathology (Charite) and the Institute of Theoretical Biology (HU Berlin).

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SPEED: (S)ignaling (P)athway (E)nrichment using (E)xperimental (D)atasets. The project is part of PhD student summer research conducted by Jignesh Parikh from the Boston University Bioinformatics Program. And Bertram Klinger from the Group of Systems Biology of Molecular Networks. The SPEED project is hosted by the Group of Systems Biology of Molecular Network. At the Laboratory of Molecular Tumor Pathology (Charite) and the Institute of Theoretical Biology (HU Berlin).

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2 download annotations

3 database statistics

4 suggest pathways

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SPEED: Home | speed.sys-bio.net Reviews

https://speed.sys-bio.net

SPEED: (S)ignaling (P)athway (E)nrichment using (E)xperimental (D)atasets. The project is part of PhD student summer research conducted by Jignesh Parikh from the Boston University Bioinformatics Program. And Bertram Klinger from the Group of Systems Biology of Molecular Networks. The SPEED project is hosted by the Group of Systems Biology of Molecular Network. At the Laboratory of Molecular Tumor Pathology (Charite) and the Institute of Theoretical Biology (HU Berlin).

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speed.sys-bio.net

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SPEED: Database Statistics

http://speed.sys-bio.net/cgi-bin/database_statistics.py

SPEED: (S)ignaling (P)athway (E)nrichment using (E)xperimental (D)atasets. The SPEED database stores z-score normalized microarray data from perturbation experiments for specific signaling pathways. All microarray data is downloaded from the Gene Expression Omnibus ( GEO. At NCBI. The GEO series for the perturbation experiments are noted per pathway.

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SPEED: Help

http://speed.sys-bio.net/help.html

SPEED: (S)ignaling (P)athway (E)nrichment using (E)xperimental (D)atasets. Running SPEED Pathway Enrichment. Downloading SPEED Signature Genes. Viewing SPEED Database Statistics. Running SPEED Pathway Enrichment:. SPEED uses a Fisher's exact test with FDR correction to identify a significant overlap between an input gene list and each of the SPEED pathway signature gene sets. The Run SPEED. For converting your gene list to an accepted format. Currently only human genes are supported. 2 Pathways to Include.

3

SPEED: Download Annotations

http://speed.sys-bio.net/cgi-bin/download_annotations.py

SPEED: (S)ignaling (P)athway (E)nrichment using (E)xperimental (D)atasets. All signature genes may be downloaded using this form. Max absolute z-score percentile:. Min percent overlap across experiments:. Max expression level percentile:. Signature genes must be unique:. Click here to download entire SPEED SQLite database and python scripts. Click here to download SPEED database tables in tab delimited text.

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SPEED: Run Speed

http://speed.sys-bio.net/cgi-bin/run_speed.py

SPEED: (S)ignaling (P)athway (E)nrichment using (E)xperimental (D)atasets. The SPEED enrichment algorithm extracts signature gene sets per pathway from microarray experiments and compares an input gene list against the signature genes using Fisher's exact test. The reported p-value is a one-tailed calculation. Multiple hypothesis correction is achieved by calculating a false discovery rate described in Blüthgen et al, Nucleic Acids Res., 2005. Please enter your gene list below (limited to 1000 IDs):.

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SPEED: Suggest Pathways

http://speed.sys-bio.net/cgi-bin/suggest.py

SPEED: (S)ignaling (P)athway (E)nrichment using (E)xperimental (D)atasets. Please use this form to suggest a new data set or pathway. The form will use your default email client. Or suggest new pathway in text box. Other, please specify:. As GEO accessions (GSE, GSM, or GDS), hyperlinks,. Or publications to suggest inclusion of data.

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bioinfo.lab.mcgill.ca

Resources - McGill Computational Biology Lab

http://bioinfo.lab.mcgill.ca/resources.html

Yu (Brandon) Xia Lab. Computational Structural and Systems Biology. Local Protein Community Finder. Protein Network Neighbor Search. SPEED: Signaling Pathway Enrichment using Experimental Datasets. For Voevodski et al. Active clustering of biological sequences", JMLR 2012. Yu (Brandon) Xia Lab Department of Bioengineering McGill University.

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SPEED: Home

SPEED: (S)ignaling (P)athway (E)nrichment using (E)xperimental (D)atasets. The project is part of PhD student summer research conducted by Jignesh Parikh from the Boston University Bioinformatics Program. And Bertram Klinger from the Group of Systems Biology of Molecular Networks. The SPEED project is hosted by the Group of Systems Biology of Molecular Network. At the Laboratory of Molecular Tumor Pathology (Charite) and the Institute of Theoretical Biology (HU Berlin).

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