GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

GeneSigDB (http://www.genesigdb.org or http://compbio.dfci.harvard.edu/genesigdb/) is a database of gene signatures that have been extracted and manually curated from the published literature. It provides a standardized resource of published prognostic, diagnostic and other gene signatures of cancer and related disease to the community so they can compare the predictive power of gene signatures or use these in gene set enrichment analysis. Since GeneSigDB release 1.0, we have expanded from 575 to 3515 gene signatures, which were collected and transcribed from 1604 published articles largely focused on gene expression in cancer, stem cells, immune cells, development and lung disease. We have made substantial upgrades to the GeneSigDB website to improve accessibility and usability, including adding a tag cloud browse function, facetted navigation and a ‘basket’ feature to store genes or gene signatures of interest. Users can analyze GeneSigDB gene signatures, or upload their own gene list, to identify gene signatures with significant gene overlap and results can be viewed on a dynamic editable heatmap that can be downloaded as a publication quality image. All data in GeneSigDB can be downloaded in numerous formats including .gmt file format for gene set enrichment analysis or as a R/Bioconductor data file. GeneSigDB is available from http://www.genesigdb.org

A novel, integrated in vitro carcinogenicity test to identify genotoxic and non-genotoxic carcinogens using human lymphoblastoid cells

Human exposure to carcinogens occurs via a plethora of environmental sources, with 70–90% of cancers caused by extrinsic factors. Aberrant phenotypes induced by such carcinogenic agents may provide universal biomarkers for cancer causation. Both current in vitro genotoxicity tests and the animal-testing paradigm in human cancer risk assessment fail to accurately represent and predict whether a chemical causes human carcinogenesis. The study aimed to establish whether the integrated analysis of multiple cellular endpoints related to the Hallmarks of Cancer could advance in vitro carcinogenicity assessment. Human lymphoblastoid cells (TK6, MCL-5) were treated for either 4 or 23 h with 8 known in vivo carcinogens, with doses up to 50% Relative Population Doubling (maximum 66.6 mM). The adverse effects of carcinogens on wide-ranging aspects of cellular health were quantified using several approaches; these included chromosome damage, cell signalling, cell morphology, cell-cycle dynamics and bioenergetic perturbations. Cell morphology and gene expression alterations proved particularly sensitive for environmental carcinogen identification. Composite scores for the carcinogens’ adverse effects revealed that this approach could identify both DNA-reactive and non-DNA reactive carcinogens in vitro. The richer datasets generated proved that the holistic evaluation of integrated phenotypic alterations is valuable for effective in vitro risk assessment, while also supporting animal test replacement. Crucially, the study offers valuable insights into the mechanisms of human carcinogenesis resulting from exposure to chemicals that humans are likely to encounter in their environment. Such an understanding of cancer induction via environmental agents is essential for cancer prevention

Antepipona assmanni nov.sp. und Antepipona aubrechti nov.sp., zwei neue Arten aus Kenia (Hymenoptera: Vespidae: Eumeninae)

Gusenleitner, J., Gusenleitner, F. (2010): Antepipona assmanni nov.sp. und Antepipona aubrechti nov.sp., zwei neue Arten aus Kenia (Hymenoptera: Vespidae: Eumeninae). Linzer biologische Beiträge 42 (1): 711-72

Antepipona ebmeri, eine neue Art aus der Äthiopis (Hymenoptera, Vespidae: Eumeninae)

Gusenleitner, J. (2011): Antepipona ebmeri, eine neue Art aus der Äthiopis (Hymenoptera, Vespidae: Eumeninae). Linzer biologische Beiträge 43 (2): 1019-1022, DOI: http://doi.org/10.5281/zenodo.532576

Über bemerkenswerte Faltenwespen aus der äthiopischen Region Teil 4 (Hymenoptera, Vespidae, Eumeninae)

Gusenleitner, J. (2007): Über bemerkenswerte Faltenwespen aus der äthiopischen Region Teil 4 (Hymenoptera, Vespidae, Eumeninae). Linzer biologische Beiträge 39 (1): 83-95, DOI: http://doi.org/10.5281/zenodo.541293

Ancistrocerus biphaleratus subsp. palaestinicus GIORDANI SOIKA 1952

Ancistrocerus biphaleratus palaestinicus GIORDANI SOIKA 1952 Ancistrocerus (Ancistrocerus) palaestinicus GIORDANISOIKA 1952 - Boll.Soc. veneziana Stor. nat. 6: 22. V e r b r e i t u n g: Israel,SaudiArabien.Published as part of Gusenleitner, J., 2013, Die Gattungen der Eumeninae im Nahen Osten, in Nordafrika und in Arabien (Hymenoptera: Vespidae: Eumeninae), pp. 5-107 in Linzer biologische Beiträge 45 (1) on page 11, DOI: 10.5281/zenodo.452608

Bemerkenswerte Faltenwespen-Funde aus der orientalischen Region Teil 5 (Hymenoptera: Vespidae, Eumeninae)

Gusenleitner, J. (2010): Bemerkenswerte Faltenwespen-Funde aus der orientalischen Region Teil 5 (Hymenoptera: Vespidae, Eumeninae). Linzer biologische Beiträge 42 (1): 695-709, DOI: http://doi.org/10.5281/zenodo.533288

Über bemerkenswerte Faltenwespen aus der äthiopischen Region Teil 5 (Hymenoptera: Vespidae: Eumeninae, Masarinae)

Gusenleitner, J. (2007): Über bemerkenswerte Faltenwespen aus der äthiopischen Region Teil 5 (Hymenoptera: Vespidae: Eumeninae, Masarinae). Linzer biologische Beiträge 39 (2): 957-968, DOI: http://doi.org/10.5281/zenodo.541703

Über bemerkenswerte Faltenwespen aus der äthiopischen Region Teil 9 (Hymenoptera: Vespidae: Eumeninae)

Gusenleitner, J. (2012): Über bemerkenswerte Faltenwespen aus der äthiopischen Region Teil 9 (Hymenoptera: Vespidae: Eumeninae). Linzer biologische Beiträge 44 (2): 1159-1176, DOI: http://doi.org/10.5281/zenodo.532900

Neue Masarinae aus der paläarktischen Region (Hymenoptera: Vespidae: Masarinae)

Gusenleitner, J. (2012): Neue Masarinae aus der paläarktischen Region (Hymenoptera: Vespidae: Masarinae). Linzer biologische Beiträge 44 (1): 319-326, DOI: 10.5281/zenodo.532732