pseudogenes in PseudoPipe

Q:
The pseudogene databases, including Pseudofam and PseudoPipe, have been extremely helpful for a project I am working on, and I was wondering if you knew how it would be possible to compare the DNA sequence of a human gene with all the pseudogenes on the PseudoPipe resources. I am looking to identify pseudogenes that may be related to the genes I am working with. I was hoping there was a way to devise this information by BLAST comparing the DNA sequence a specific gene with the sequences from all the pseudogenes in the genome, similar to NCBI BLAST or UniProt BLAST feature.

Any help or insight would be appreciated.

A:
If you have many genes to query, may be you can use BLAST+ (https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) to build your own tool. You can then download the sequences of all pseudogenes and make a BLAST database (https://www.ncbi.nlm.nih.gov/books/NBK279688/ ) from which you can query.

ASE analysis within your article (A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals)

Q:
I am writing to your regarding the code to analyse ASE in RNA-seq data present within this Article, specifically the beta diversity evaluation and application test. I was wondering if the code is available, I would like to apply it compare samples.

A:
The code for calling allele-specific sites is available at
https://github.com/gersteinlab/alleleDB

The specific scripts for the beta-binomial test are
alleledb_calcOverdispersion.R
alleledb_alleleseqBetabinomial.R

Question regarding RNA-seq data uploaded to “Synapse”

Q:
I was referred to you by Micheal Gandal for a question I have regarding you RNA-seq data from the fascinating shared article "Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder"

I know you’ve uploaded the TPM data to to PsychEncode website – could you tell me if the data this file is normalized DER-02_PEC_Gene_expression_matrix_TPM

A:
We didn’t run any quantile normalization on this file.

Request about Pubnet

Q:
I am looking for an easy-to-handle application to analyse collaborative networks in science, and I am very interested by Pubnet, that you published quite a while ago. Unfortunately, event if it looks very simple to use the web interface, after submitting a query with a author name, I always have a page indicating the pubmed xml was generated, but it is never analysed. It always blocks as this: (see image)

A:
We’ve managed to revive pubnet. Please check it out.

http://pubnet.gersteinlab.org

Running FunSeq

Q:
I recently read your paper on Funseq, and I am pretty interested in using it in solving some of my interested questions regarding cortex plasticiy. However, I’m not very familiar with Linux/UNIX running environment for this software, and what I have is just a mac laptop….Could you give me some information about how I could use this software on a mac computer, or where I could find some useful information instructing me how I could use this software on a mac computer?

A:
You should be able to download this software on a mac and use it.
You can download it from funseq.gersteinlab.org.

Since you are not familiar with downloading software, have you tried to use the online version at http://funseq.gersteinlab.org/analysis .
You can upload your file and see what you get.

Asking or data used in finding processed psedogenes in the human genome

Q:
Recently, I was reading one of your papers about finding processed pseudogenes published in 2003: "Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome". Because I want to find processed pseudogenes among several recently released mammalian genomes. Your paper is very interesting and helpful for my work. And to ensure the method i grasped is correct, I want to use your original data to redo your analysis process.

But I come across a problem when I download nonredundant human proteome set from the EBI Web site. Because the data was published in June 2002, and I can’t successfully download them from EBI website. Here I write to you with the hope of getting nonredundant human proteome set you used released in June 2002. Although I know many years have passed since the paper was published and you may also lost the original data, I still want to have a try!

A:
The data associated with the paper is here: http://pseudogene.org/human-all/index.html. You can also find the latest human pseudogene annotation here: http://pseudogene.org/Human/

HingeAtlas (2007)

Q:
I am reading your Hinge Atlas (2007) paper.
I searched for your dataset to study the pdb structures you used and their
hinge residues, but I could not download it from the page:
http://molmovdb.org/cgi-bin/sets.cgi.
Could you please send a file if it is possible by email, or please check and
fix if there is a bug on the web page.

A:
Please try the Hinge Atlas Gold while we investigate the webpage. This may take time.

MS data in the Psychencode datasets

Q1:
I recently met you at LMB where you gave a wonderful talk on PsychENCODE data analysis.

You mentioned that there were MS datasets in the PsychENCODE. I am unable to find it. Is it possible for you to point me to that or point me to someone who may know about this? Is it possible for you to point out the MS data in the PschENCODE datasets?

A2:
Could you please explain a little more about what dataset you need?

Q2:
I am looking for Mass Spec data sets in PsychEncode. Mark mentioned that MS analysis were done for some samples. I wonder whether you could help me in identifying them?

A2:
I just checked with our DCC team and currently we don’t have any Mass Spec data available for public sharing.

Q3:
What is dcc team? I was given to believe from the publications that this data was available along with others for analysis. i would not have asked otherwise. is there a way i can reach out to any group among your dcc team that has this data to see whether i can formally collaborate with them? Can you kindly let me know who may be the best person to ask for the details of the group that may have the MS datasets? I am looking for MS data (even if it is published) from any of the samples that were used in the Psychencode project.
I am willing to collaborate and share authorships with the scientists who generated these datasets?
Would it be possible for you to point out to any one whom you may know who may have this dataset (published or unpublished)?

A3:
I have contacted the group that is generating the Mass Spec data. Are you specifically interested in proteomics related to donors with neuropsychiatric disorders? We (Sage Bionetworks) also function as the data coordination center for the NIA funded Accelerating Medicines Partnership – Alzheimer’s Disease (AMP-AD). There are a variety of studies in AMP-AD with Mass Spec proteomics on post mortem brain tissue, that also have other genomic data such as WGS and RNAseq. Included in that is the Religious Orders Study and Memory and Aging project (ROS/MAP) from the Rush Alzheimer’s Disease Center. See here for information on the cohorts. There will be TMT labeled MS on ~400 ROS/MAP donors released this fall.

Q4:
Thank you for getting in touch with me. Thank you for your pointer. Indeed, we will be interested in the Alzheimer’s samples (all the three WGS, RNAseq and Proteomics).
I will write a separate note to you on this.
At the moment, we are looking for MS samples from donors with neuropsychiatric disorders.

A4:
Actually, my lab is doing something very similar as well, validating novel ORFs identified from our third generation sequencing, and riboseq data.
If you use other approaches that we did not use yet, or with some special goals more than just validating ORFs in brain, I will be happy to collaborate.
I have two students/collaborators on this.

Q5:
Is it possible for me to make a quick call?

A5:
…(resolved via phone call on Jul 9, 2019)…