castanyes blaves

Random ramblings about some random stuff, and things; but more stuff than things -- all in a mesmerizing and kaleidoscopic soapbox-like flow of words.



Ensembl GeneTree for SATB1 (Special AT-rich sequence-binding protein 1)

Breast cancer 'master gene' breakthrough

The breakthrough paves the way for the development of drugs which could
halt the progress of the disease and help save the lives of some of the
44,000 women diagnosed with the illness every year.

This is the Ensembl GeneTree for the SATB1 and SATB2 genes, showing the evolutionary history of this two genes along the different species in Ensembl:

If shows the fish whole-genome-duplication effect on SATB2, and there is an extra copy as outgroup of SATB2 that is probably pulled there by a bad Tetraodon prediction in SATB1. These may be corrected once the Tetraodon gene build is updated. The insects and C.elegans are outgroups, suggesting a whole-genome-duplication event after the split with the Bilateria.

There is a very small Macaca mulatta prediction. Also a split gene prediction for platypus, involving two
transcripts that are next to each other in the Ultracontig 239, and should probably be merged
into the same gene. The surrounding genes match correctly:

The Treefam tree predicts a duplication in the C.elegans genome (highlighted in blue), compared to C.briggsae and C.remanei:

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Ensembl GeneTrees for SIRT1 and DBC1

DBC1 is a negative regulator of SIRT1

This are the Ensembl GeneTrees for the SIRT and FAM5A/B/C (DBC1) families, showing the evolutionary history of these genes in the different species present in the Ensembl database:

The SIRT family contains SIRT1, SIRT6 and SIRT7, SIRT4, SIRT5 and SIRT2 and SIRT3. They have one common yeast outgroup, and two other yeast outgroups for some subfamilies, and each subfamily contains outgroups to Ciona or insects and/or C. elegans.

SIRT1 seems to be very basal and conserved with respect to the others, followed by SIRT2 and SIRT3.
SIRT7, on the other side, seems to have evolved faster when compared to the other subfamilies: it contains an extra peptide stretch at the end that none of the other subfamilies has.

For DBC1, we see conservation down to the Euteleostomi (bony vertebrates) level, with the fish Whole-Genome-Duplication very apparent at the top of the GeneTree:

A few gene predictions are partial and so misplaced in the tree, with a very apparent Danio rerio gene (NSDARG00000061051) and some 2x species. In this case, the DBC1 subfamily is the one with the longest internal branch length compared to the other two, and although this could be due to some partial gene predictions influencing the alignment, the alignment for the (non-2x) amniotes looks very good:

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Ensembl GeneTree SLC2A (Soluyte Carrier Family 2)

The gene variation found in the SLC2A gene appears to make it harder for the body to remove uric acid from the blood.

This is the Ensembl GeneTree for the SLC2A family, comprising about 500 proteins along the whole Fungi/Metazoa Tree and showing the evolutionary history of these genes in the different species present in the Ensembl database:

We can see that most of the subtrees define the different members of the family: SLC2A12, SLC2A10, SLC2A9, SLC2A11, SLC2A5, SLC2A7, SLC2A14, SLC2A1, SLC2A4, SLC2A2, SLC2A8, SLC2A6 and SLC2A13. Treefam contains separate Gene Trees for most of them, based on the presence of a deep outgroup like yeast or some other outgroup species.

The gene is present in yeast, also in Arabidopsis and rice (Treefam), and seems to have duplicated after the split of these outgroup species in both lineages.

SLC2A10 and SLC2A12 seem to be more recently related to each other and our tree places this duplication at the Euteleostomi level. Treefam places a rice gene as an outgroup, but this could be an artifact. A lot of the yeast genes seem to cluster together, but it's not clear if this is consistent or not.

The Ensembl MCL Family for SLC2A10 clusters a lot of human genes, all of them located at one arm of chr20 (below). This is conserved for Pongo pygmaeus, where we also see then in chr20:

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Ensembl GeneTree PARP (Poly (ADP-ribose) polymerase)

Loss of BRCA2 function impairs DNA repair by homologous recombination and renders cells particularly sensitive to cisplastin and also to PARP (poly (ADP-ribose) polymerase) inhibitors.

This is the Ensembl GeneTree for the PARP family, comprising PARP1, PARP2 and PARP3, showing the evolutionary history of these genes in the different species present in the Ensembl database:

The genetree shows one C.elegans outgroup, Y71F9AL.18, and places the insect outgroups in the PARP1 subtree, although they should probably be outgroups of all PARP genes. Treefam has the families split into PARP1, PARP2, PARP3 and so on. In the Treefam full trees, only PARP1 contains the 12 Drosophilas outgroup, in agreement with our tree, suggesting that the duplication was after the split with the insects, and PARP1 is still closer to the ancestral gene. The gene predictions for the two Cionas are not perfect, and one copy goes to PARP2 where should probably go to PARP1. There is only a Ciona savigny and no Ciona intestinalis for PARP1. There is one Tetraodon nigroviridis gene that is probably mispredicted: GSTENG00030378001, and hopefully will get better with the upcoming new gene build.

We can't see a fish-WGD effect on this tree, so the redundant copies where potentially lost after the duplication.

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Compiz Fusion keyboard shortcuts

SUPER+SHIFT+C = clear fire
CTRL+ALT+LEFT ARROW = rotate cube
CTRL+ALT+DOWN ARROW = flat desktop
SHIFT+ALT+UP = initiate window picker
CTRL+ALT+DOWN = unfold cube
ALT+TAB = window switch
SUPER+TAB = flip switcher or ring switcher, depending on which is enabled.
ALT+F7 = initiate 'move windows'
SHIFT+F9 = water effect
SHIFT+F10 = slow animations
CTRL+ALT+D = show desktop

For Grouping and Tabbing:
SUPER+S = select single window
SUPER+T = tab group
SUPER+Left = change left tab
SUPER+Right = change right tab
SUPER+G = group windows
SUPER+U = ungroup windows
SUPER+R = remove group window
SUPER+C = close group
SUPER+X = ignore group
Hold the SUPER button then select the windows you want to group and then hit SUPER+G.

The SUPER key is the Windows key on most keyboards.


Second debate, second round of conclusions

Zapatero vence a Rajoy (El País)
Rajoy gana también el segundo asalto pese al juego sucio de Zapatero (Libertad Digital)



Ensembl GeneTree TARDBP (TDP-43)

Researchers say they have made the most significant breakthrough for 15 years in the quest to understand the fatal condition Motor Neurone Disease (MND).

This is the Ensembl GeneTree for the TARDBP family, showing the evolutionary history of these genes in the different species present in the Ensembl database:

This tree shows the effect of a whole-genome-duplication (WGS) in the fish genomes, resulting in two copies of it in each of the five fish genomes in Ensembl v48. There is a duplication in Drosophila melanogaster, that may have taken place before the speciation of the melanogaster subgroup (D.melanogaster,D.simulans,D.sechellia).

There are 3 extra duplications, one in Dog, one in Monodelphis and a double duplication in Macaca mulatta. Preliminary data seems to indicate that the double duplication is also present in the orang genome, which isn't a very parsimonious occurrence. If we consider
that the duplication took place at the Catarrhini level, it requires three gene loss events in Human and three more in Chimp to explain why we see four copies in the rhesus and orang genomes. All of them seem like real genes, without much doubt about their prediction.

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Mango-lassi desktop sharing Ubuntu

sudo apt-get install libavahi-ui0
sudo alien mango-lassi-000-6.2.i586.rpm
sudo dpkg -i mango-lassi_000-7.2_i386.deb


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