Search Preview
Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis | L. Collado-Torres
lcolladotor.github.ioGenome-wide association studies have identified 108 schizophrenia risk loci, but biological mechanisms for individual loci are largely unknown. Using developmental, genetic and illness-based RNA sequencing expression analysis in human brain, we characterized the human brain transcriptome around these loci and found enrichment for developmentally regulated genes with novel examples of shifting isoform usage across pre- and postnatal life. We found widespread expression quantitative trait loci (eQTLs), including many with transcript specificity and previously unannotated sequence that were independently replicated. We leveraged this general eQTL database to show that 48.1% of risk variants for schizophrenia associate with nearby expression. We lastly found 237 genes significantly differentially expressed between patients and controls, which replicated in an independent dataset, implicated synaptic processes, and were strongly regulated in early development. These findings together offer genetics- and diagnosis-related targets for better modeling of schizophrenia risk. This resource is publicly available at http://eqtl.brainseq.org/phase1.
.io > lcolladotor.github.io
SEO audit: Content analysis
| Language | Error! No language localisation is found. | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Title | Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis | L. Collado-Torres | ||||||||||||||||||||||||||||||||||||
| Text / HTML ratio | 32 % | ||||||||||||||||||||||||||||||||||||
| Frame | Excellent! The website does not use iFrame solutions. | ||||||||||||||||||||||||||||||||||||
| Flash | Excellent! The website does not have any flash contents. | ||||||||||||||||||||||||||||||||||||
| Keywords cloud | loci schizophrenia found risk expression human replicated transcriptome brain genetic regulated genes ColladoTorres patients controls expressed variants differentially independent dataset | ||||||||||||||||||||||||||||||||||||
| Keywords consistency |
|
||||||||||||||||||||||||||||||||||||
| Headings |
|
||||||||||||||||||||||||||||||||||||
| Images | We found 0 images on this web page. |
SEO Keywords (Single)
| Keyword | Occurrence | Density |
|---|---|---|
| loci | 4 | 0.20 % |
| schizophrenia | 4 | 0.20 % |
| found | 3 | 0.15 % |
| risk | 3 | 0.15 % |
| expression | 3 | 0.15 % |
| human | 3 | 0.15 % |
| replicated | 2 | 0.10 % |
| transcriptome | 2 | 0.10 % |
| brain | 2 | 0.10 % |
| genetic | 2 | 0.10 % |
| regulated | 2 | 0.10 % |
| genes | 2 | 0.10 % |
| ColladoTorres | 2 | 0.10 % |
| patients | 1 | 0.05 % |
| controls | 1 | 0.05 % |
| expressed | 1 | 0.05 % |
| variants | 1 | 0.05 % |
| differentially | 1 | 0.05 % |
| independent | 1 | 0.05 % |
| dataset | 1 | 0.05 % |
SEO Keywords (Two Word)
| Keyword | Occurrence | Density |
|---|---|---|
| human brain | 2 | 0.10 % |
| schizophrenia risk | 2 | 0.10 % |
| the human | 2 | 0.10 % |
| Toggle navigation | 1 | 0.05 % |
| expressed between | 1 | 0.05 % |
| associate with | 1 | 0.05 % |
| with nearby | 1 | 0.05 % |
| nearby expression | 1 | 0.05 % |
| expression We | 1 | 0.05 % |
| We lastly | 1 | 0.05 % |
| lastly found | 1 | 0.05 % |
| found 237 | 1 | 0.05 % |
| 237 genes | 1 | 0.05 % |
| genes significantly | 1 | 0.05 % |
| significantly differentially | 1 | 0.05 % |
| differentially expressed | 1 | 0.05 % |
| between patients | 1 | 0.05 % |
| for schizophrenia | 1 | 0.05 % |
| patients and | 1 | 0.05 % |
| and controls | 1 | 0.05 % |
SEO Keywords (Three Word)
| Keyword | Occurrence | Density | Possible Spam |
|---|---|---|---|
| Toggle navigation L | 1 | 0.05 % | No |
| expressed between patients | 1 | 0.05 % | No |
| schizophrenia associate with | 1 | 0.05 % | No |
| associate with nearby | 1 | 0.05 % | No |
| with nearby expression | 1 | 0.05 % | No |
| nearby expression We | 1 | 0.05 % | No |
| expression We lastly | 1 | 0.05 % | No |
| We lastly found | 1 | 0.05 % | No |
| lastly found 237 | 1 | 0.05 % | No |
| found 237 genes | 1 | 0.05 % | No |
| 237 genes significantly | 1 | 0.05 % | No |
| genes significantly differentially | 1 | 0.05 % | No |
| significantly differentially expressed | 1 | 0.05 % | No |
| differentially expressed between | 1 | 0.05 % | No |
| between patients and | 1 | 0.05 % | No |
| variants for schizophrenia | 1 | 0.05 % | No |
| patients and controls | 1 | 0.05 % | No |
| and controls which | 1 | 0.05 % | No |
| controls which replicated | 1 | 0.05 % | No |
| which replicated in | 1 | 0.05 % | No |
SEO Keywords (Four Word)
| Keyword | Occurrence | Density | Possible Spam |
|---|---|---|---|
| Toggle navigation L ColladoTorres | 1 | 0.05 % | No |
| expressed between patients and | 1 | 0.05 % | No |
| schizophrenia associate with nearby | 1 | 0.05 % | No |
| associate with nearby expression | 1 | 0.05 % | No |
| with nearby expression We | 1 | 0.05 % | No |
| nearby expression We lastly | 1 | 0.05 % | No |
| expression We lastly found | 1 | 0.05 % | No |
| We lastly found 237 | 1 | 0.05 % | No |
| lastly found 237 genes | 1 | 0.05 % | No |
| found 237 genes significantly | 1 | 0.05 % | No |
| 237 genes significantly differentially | 1 | 0.05 % | No |
| genes significantly differentially expressed | 1 | 0.05 % | No |
| significantly differentially expressed between | 1 | 0.05 % | No |
| differentially expressed between patients | 1 | 0.05 % | No |
| between patients and controls | 1 | 0.05 % | No |
| variants for schizophrenia associate | 1 | 0.05 % | No |
| patients and controls which | 1 | 0.05 % | No |
| and controls which replicated | 1 | 0.05 % | No |
| controls which replicated in | 1 | 0.05 % | No |
| which replicated in an | 1 | 0.05 % | No |
Internal links in - lcolladotor.github.io
Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia
Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia | L. Collado-Torres
Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia | L. Collado-Torres
Non-coding Class Switch Recombination-related transcription in human normal and pathological immune responses
Non-coding Class Switch Recombination-related transcription in human normal and pathological immune responses | L. Collado-Torres
Non-coding Class Switch Recombination-related transcription in human normal and pathological immune responses | L. Collado-Torres
Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis
Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis | L. Collado-Torres
Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis | L. Collado-Torres
recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations]
recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations] | L. Collado-Torres
recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations] | L. Collado-Torres
Reproducible RNA-seq analysis using recount2
Reproducible RNA-seq analysis using recount2 | L. Collado-Torres
Reproducible RNA-seq analysis using recount2 | L. Collado-Torres
Flexible expressed region analysis for RNA-seq with derfinder
Flexible expressed region analysis for RNA-seq with derfinder | L. Collado-Torres
Flexible expressed region analysis for RNA-seq with derfinder | L. Collado-Torres
More Publications
Publications | L. Collado-Torres
Publications | L. Collado-Torres
Divergent neuronal DNA methylation patterns across human cortical development: Critical periods and a unique role of CpH methylation
Divergent neuronal DNA methylation patterns across human cortical development: Critical periods and a unique role of CpH methylation | L. Collado-Torres
Divergent neuronal DNA methylation patterns across human cortical development: Critical periods and a unique role of CpH methylation | L. Collado-Torres
Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome
Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome | L. Collado-Torres
Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome | L. Collado-Torres
More Talks
Talks | L. Collado-Torres
Talks | L. Collado-Torres
From learning to using to teaching to developing R
From learning to using to teaching to developing R | L. Collado-Torres
From learning to using to teaching to developing R | L. Collado-Torres
Reproducible RNA-seq analysis with recount and recount-brain
Reproducible RNA-seq analysis with recount and recount-brain | L. Collado-Torres
Reproducible RNA-seq analysis with recount and recount-brain | L. Collado-Torres
More Posts
Posts | L. Collado-Torres
Posts | L. Collado-Torres
rstats
Rstats | L. Collado-Torres
Rstats | L. Collado-Torres
Science
Why I applied to join SNI: the Mexican National Researchers registry
Science | L. Collado-Torres
Science | L. Collado-Torres
Misc
Problems with an article from the Baltimore Sun covering Dr. Mahoney-Steel’s immigration issues
Misc | L. Collado-Torres
Misc | L. Collado-Torres
CONTINUE READING
Problems with an article from the Baltimore Sun covering Dr. Mahoney-Steel’s immigration issues | L. Collado-Torres
Problems with an article from the Baltimore Sun covering Dr. Mahoney-Steel’s immigration issues | L. Collado-Torres
Ideas
What about a lawyer-like app as the minimum help for defendants in immigration cases?
Ideas | L. Collado-Torres
Ideas | L. Collado-Torres
CONTINUE READING
What about a lawyer-like app as the minimum help for defendants in immigration cases? | L. Collado-Torres
What about a lawyer-like app as the minimum help for defendants in immigration cases? | L. Collado-Torres
here
MPH TA sessions
MPH TA sessions
Analysis of High-Throughput Sequencing data with Bioconductor
L. Collado Torres: PDCB-HTS
L. Collado Torres: PDCB-HTS
Introduction to R and Biostatistics
L. Collado Torres: PDCB-Biostats
L. Collado Torres: PDCB-Biostats
Introduction to R for bench biologists
L. Collado Torres: R Intro for Bench Biologists
L. Collado Torres: R Intro for Bench Biologists
Métodos Estadísticos y Analíticos de Datos Genómicos
L. Collado Torres: MEyAdDG
L. Collado Torres: MEyAdDG
backup
R/Bioconductor. Curso Intensivo Oct-Nov 2008
R/Bioconductor. Curso Intensivo Oct-Nov 2008
backup
Principios de EstadÃstica. Feb-Jun 2009
Principios de EstadÃstica. Feb-Jun 2009
backup
Seminario III: R/Bioconductor. Ago-Dic 2009
Seminario III: R/Bioconductor. Ago-Dic 2009
this post
How to ask for help for Bioconductor packages | L. Collado-Torres
How to ask for help for Bioconductor packages | L. Collado-Torres
Lcolladotor.github.io Spined HTML
Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis | L. Collado-Torres Toggle navigation L. Collado-Torres Home Publications Talks Blog CV Students Teaching Contact Search Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis Jaffe AE, Straub R, Shin JH, Tao R, Gao Y, Collado-Torres L, Kam-Thong T, Xi HS, Quan J, Chen Q, Colantuoni C, Ulrich WS, Maher BJ, Deep-Soboslay A, The BrainSeq Consortium, Cross AJ, Brandon NJ, Leek JT, Hyde TM, Kleinman JE, Weinberger DR Abstract Genome-wide undertone studies have identified 108 schizophrenia risk loci, but biological mechanisms for individual loci are largely unknown. Using developmental, genetic and illness-based RNA sequencing expression wringer in human brain, we characterized the human smart-ass transcriptome virtually these loci and found enrichment for developmentally regulated genes with novel examples of shifting isoform usage wideness pre- and postnatal life. We found widespread expression quantitative trait loci (eQTLs), including many with transcript specificity and previously unannotated sequence that were independently replicated. We leveraged this unstipulated eQTL database to show that 48.1% of risk variants for schizophrenia socialize with nearby expression. We lastly found 237 genes significantly differentially expressed between patients and controls, which replicated in an self-sustaining dataset, implicated synaptic processes, and were strongly regulated in early development. These findings together offer genetics- and diagnosis-related targets for largest modeling of schizophrenia risk. This resource is publicly misogynist at http://eqtl.brainseq.org/phase1. Type Peer-reviewed Publication Nature Neuroscience Date July, 2018 Links PDF Project Pre-print © 2011-2018 Leonardo Collado Torres under (CC) BY-NC-SA 4.0. All thoughts and opinions here are my own. · Powered by the Academic theme for Hugo. × Cite Copy Download