User: Andrei Kucharavy

Reputation:
10
Status:
New User
Location:
Switzerland/Lausanne/EPFL
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 4 days ago
Joined:
6 years, 1 month ago
Email:
a***************@gmail.com

Systems network biology computational biologist with a heavy penchant for theoretical computer science and random networks theory.

Posts by Andrei Kucharavy

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Looking for Yeast transcription factor - target gene matrix with weights (activa
... Yes - Yeastract only have binary matrixes available for downloads, whereas Jaspar is more about transcription factors binding profiles than it is about regulatory interactions towards specific genes. ...
written 4 weeks ago by Andrei Kucharavy10
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Looking for Yeast transcription factor - target gene matrix with weights (activations, correlations, ...)
... I am currently looking for a matrix of transcription factors impact on genes in yeast. For now, all the compendiums I am finding, only show binary data (presence/absence of a regulatory relationship), whereas for what I am doing I need continuous data - such as activation scores, percentage of exp ...
database transcription factors yeast written 4 weeks ago by Andrei Kucharavy10
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Proteomics - gene covariates for iBAQ measurements.
... I am currently looking into analyzing proteomics data, summarized as iBAQ counts. One of the things I was wondering about was whether iBAQ counts for genes presented any covariation (such as for instance CG content in genes for sequencing). If yes, where the tables for such covariation can be found ...
proteomics ibaq written 16 months ago by Andrei Kucharavy10
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Uniport-sprot hash digests
... I am looking for a place to find the Uniprot-Sprot.dat hash digests to verify the integrity of files upon download. Given how frequently this file is updated, I can't just store and re-use existing hashes, but instead need to find a place online that stores them. ...
swissprot uniprot written 3.6 years ago by Andrei Kucharavy10 • updated 3.6 years ago by SES8.2k
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Comment: C: Database to map gene ID to the chromosome where it is located?
... Hello Summer, hope you are doing well there! Cf my answer, hope it helps. ...
written 4.3 years ago by Andrei Kucharavy10
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Answer: A: Database to map gene ID to the chromosome where it is located?
... It seems that Uniprot has "Proteomes" object some of which actually map to the chromosomes. In Uniprot, this is availabe under the "DR;    EMBL; BKXXXXX; ... ;. .. ;..." field (for yeast, CMXXXX for humans).  A mapping from BKXXX (CMXXX) references seems to be obtainable manually from the Uniprot ...
written 4.3 years ago by Andrei Kucharavy10
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Comment: C: Database to map gene ID to the chromosome where it is located?
... Could you be a little bit more explicit?   ...
written 4.3 years ago by Andrei Kucharavy10
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Comment: C: Database to map gene ID to the chromosome where it is located?
... Thank you for your answer! I see there is a way to do the same thing for the mouse thanks to the same resource. Is there a way to retrieve the mapping for Saccharomyces Cerevisiae? ...
written 4.3 years ago by Andrei Kucharavy10
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Database to map gene ID to the chromosome where it is located?
... I am looking for a database, preferentially with a .csv or .txt dump that would be able to convert gene accession handles (Name, Gene Id, UNIPROT IDs, EMBL accession numbers, ...)  to the chromosomes they are assigned in their specific organism. This data is usually shown in web rendering of the Un ...
gene written 4.3 years ago by Andrei Kucharavy10

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Autobiographer 4 weeks ago, has more than 80 characters in the information field of the user's profile.
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Database to map gene ID to the chromosome where it is located?

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