Monthly Archives: March 2014

Resource: The COMPARTMENTS database on protein subcellular localization

Together with collaborators in the groups of Seán O’Donoghue and Reinhard Schneider, my group has recently launched a new web-accessible database named COMPARTMENTS.

COMPARTMENTS unifies subcellular localization evidence from many sources by mapping all proteins and compartments to their STRING identifiers and Gene Ontology terms, respectively. We import curated annotations from UniProtKB and model organism databases and assign confidence scores to them based on their evidence codes. For human proteins, we similarly import and score evidence from The Human Protein Atlas. COMPARTMENTS also uses text mining to derive subcellular localization evidence from co-occurrence of proteins and compartments in Medline abstracts. Finally, we precompute subcellular localization predictions with the sequence-based methods WoLF PSORT and YLoc. For further details, please refer to our recently published paper entitled “COMPARTMENTS: unification and visualization of protein subcellular localization evidence”.

To provide a simple overview of all this information, we visualize the combined localization evidence for each protein onto a schematic of an animal, fungal, or plant cell:




You can click any of the three images above to go to the COMPARTMENTS web resource. To facilitate use in large-scale analyses, the complete datasets for major eukaryotic model organisms are available for download.

Announcement: PTMs in Cell Signaling conference

Two years ago, I was one of the organizers of the 2nd Copenhagen Bioscience Conference entitled PTMs in Cell Signaling. I think it is fair to describe it as a highly successful meeting, and it is my great pleasure to announce that we will be organizing a second meeting on the topic September 14-18, 2014.

CBC6 poster

My co-chairs Jeremy Austin Daniel, Michael Lund Nielsen, and Amilcar Flores Morales have managed to put together the following excellent lineup of invited speakers:

Alfonso Valencia, Chris Sander, David Komander, Gary Nolan, Genevieve Almouzni, Guillermo Montoya, Hanno Steen, Henrik Daub, John Blenis, John Diffley, John Tainer, Karolin Luger, Marcus Bantscheff, Margaret Goodell, Matthias Mann, Michael Yaffe, Natalie Ahn, Pedro Beltrao, Stephen Elledge, Tanya Paull, Tony Hunter, Yang Shi, Yehudit Bergman, and Yosef Shiloh.

All conference expenses are covered, which means that there will be no registration fee and no expenses for accommodation or food. You will have to cover your own travel expenses, though.

Participants will be selected based on abstract submission, which is open until June 9, 2014. For more information please see the conference website.

Commentary: Are other women a woman’s worst enemies in science?

It is clear that in science, we have a gender bias among leaders. It is my impression that most people think this is due to a combination of men and women having different priorities in life and high-ranking male professors favoring their own gender. Conversely, I have never heard anyone dare to suggest that women may be their own worst enemies in this context.

Benenson and coworkers from Emmanuel College have just published an interesting study in Current Biology on collaborations between full professors and assistant professors entitled “Rank influences human sex differences in dyadic cooperation”.

By tabulating the joint publications, they found 76 same-sex publications from male full professors, which should be compared to a random expectation of 61 such publications. By contrast they found only 14 same-sex publications from female full professors with the random expectation being 29. In other words, whereas male full professors collaborated 25% more with male assistant professors than expected, female full professors collaborated more than 50% less with female assistant professors than expected. The authors conclude:

Our results are consistent with observations suggesting that social structure takes differing forms for human males and females. Males’ tendency to interact in same-gender groups makes them more prone to cooperation with asymmetrically ranked males. In contrast, females’ tendency to restrict their same-gender interactions to equally ranked individuals make them more reluctant to cooperate with asymmetrically ranked females.

There is, in other words, a bias towards high-ranking professors of both genders to preferentially collaborate with lower-ranking male professors as opposed to lower-ranking female professors. If anything, that bias appears to be stronger in case of high-ranking female professors than high-ranking male professors.