Minor fixes to earlier pages and first attempt at adding hover and qu…

…estion mark text. (#20)

* Minor fixes to earlier pages and first attempt at adding hover and question mark text.

* Pushed constraint to issue

* Minor fixes to the hover text.

* Update src/browsers/schema/content/homepage.md

* Resolved changes.

* Deleted results.md

src/browsers/schema/content/about.md

@@ -6,7 +6,7 @@ The Schizophrenia Exome Sequencing Meta-analysis (SCHEMA) consortium is a large
 
 The SCHEMA Phase I dataset (GRCh37/hg19) contains the analysis of exomes from 24,248 cases and 97,322 controls, and _de novo_ mutations from 3,402 parent-proband trios. Our study has actively recruited from diverse global populations, and includes individuals of European, Latin American, East Asian, Ashkenazi Jewish, and African American ancestry. Because the sequence data was generated with various capture technologies over a span of seven years, we adapted and developed methods to reduce possible confounders, and incorporated this information during the quality control and analysis steps. The first results have provided genome-wide significant results associating ultra-rare protein-coding variants in individual genes to risk of schizophrenia. Later releases are planned with larger number of samples that will further increase power, and will be released here before any publication.  
 
-We would also like to thank the many tens of thousands of patients and families who generously contributed to our effort. This project is made possible by the generosity of many funders, including the [Stanley Foundation](https://www.broadinstitute.org/stanley), [National Institutes of Mental Health (NIMH)](https://www.nimh.nih.gov/index.shtml), Kent and Elizabeth Dauten, and The Dalio Foundation, and the leadership of its members.  
+We would like to thank the many tens of thousands of patients and families who generously contributed to our effort. This project is made possible by the generosity of many funders, including the [Stanley Family Foundation](https://www.broadinstitute.org/stanley), [National Institutes of Mental Health (NIMH)](https://www.nimh.nih.gov/index.shtml), [National Human Genome Research Institute (NHGRI)](https://www.genome.gov/), [Kent and Elizabeth Dauten Foundation](https://dautenbipolarcenter.org/about/dauten-family), the [Dalio Foundation](https://www.daliophilanthropies.org/initiatives/mental-health-and-wellness/), and the leadership of its members.  
 
 ## Contributing scientists  
 
@@ -44,7 +44,7 @@ Tim B. Bigdeli, Michael Boehnke, Evelyn J. Bromet, Peter F. Buckley, Michael A.
 
 We would like to thank the patients and families who participated in our studies in the past two decades, without whom our research and findings would not be possible. Research reported in this publication was supported by the National Institute of Mental Health, and the National Human Genome Research Institute of the National Institutes of Health under award numbers: U01MH10564, U01MH105578, R01MH085548 and U54HG003067.  
 
-We would also like to acknowledge the generous support from the Stanley Family Foundation, Kent and Elizabeth Dauten, and The Dalio Foundation who have enabled us to rapidly expand our data generation collections with the goal of moving towards better treatments for schizophrenia and other psychiatric disorders.   
+We would also like to acknowledge the generous support from the [Stanley Family Foundation](https://www.broadinstitute.org/stanley), the [Kent and Elizabeth Dauten Foundation](https://dautenbipolarcenter.org/about/dauten-family), and the [Dalio Foundation](https://www.daliophilanthropies.org/initiatives/mental-health-and-wellness/) who have enabled us to rapidly expand our data generation collections with the goal of moving towards better treatments for schizophrenia and other psychiatric disorders.   
 
 
 

src/browsers/schema/content/generesults.md

@@ -0,0 +1,9 @@
+# Gene results description [question mark]
+
+This table displays aggregated case-control and _de novo_ counts for the purposes of gene discovery. We first enriched for pathogenic variants by restricting our analysis to ultra-rare protein-coding variants (defined as minor allele count [MAC] ≤ 5) in our data set.  
+
+Given empirically observed exome-wide burden, we focused on protein-truncating or putatively loss-of-function variants (PTVs), defined as stop-gained, frameshift, and essential splice donor or acceptor variants. We additionally analyzed damaging missense variants as prioritized by the MPC pathogenicity score (see [Samocha _et al_. 2017](https://www.biorxiv.org/content/10.1101/148353v1)).   
+
+PTVs and MPC > 3 missense variants (defined as Class I variants) were jointly analyzed in a single case-control burden test. MPC 2 - 3 variants (defined as Class II variants) were analyzed in a separate burden test before meta-analyzed with the Class I burden P-value using Stouffer's weighted Z-score method. Case-control significance was evaluated using a permutation-based Fisher's Exact Test. For genes with case-control P-value < 0.01, _de novo_ Class I and II P values were calculated using the Poisson rate test and meta-analyzed with our case-control test statistic using a Stouffer's weighted Z-score method. The Q-value is the P-value adjusted for the False Discovery Rate.
+
+For a full description and justification of the approach, please consider the main text and supplementary materials and methods of the SCHEMA pre-print manuscript.  

src/browsers/schema/content/homepage.md

@@ -4,6 +4,6 @@ The Schizophrenia Exome Sequencing Meta-analysis (SCHEMA) consortium is a large
 
 The Phase I data set (GRCh37/hg19) contains the analysis of exomes from 24,248 cases and 97,322 controls, and _de novo_ mutations from 3,402 parent-proband trios. These results have pinpointed genome-wide significant results associating ultra-rare protein-coding variants in individual genes to risk of schizophrenia.  
 
-We would also like to thank the many tens of thousands of patients and families who generously contributed to our effort. This project is made possible by the generosity of many funders, including the [Stanley Foundation](https://www.broadinstitute.org/stanley), and [National Institutes of Mental Health (NIMH)](https://www.nimh.nih.gov/index.shtml), and the leadership of its members. The [contributing groups](/about) and the [terms of use](/terms) are listed in separate pages.
+We would like to thank the many tens of thousands of patients and families who generously contributed to our effort. This project is made possible by the generosity of many funders, including the [Stanley Family Foundation](https://www.broadinstitute.org/stanley), [National Institutes of Mental Health (NIMH)](https://www.nimh.nih.gov/index.shtml), [National Human Genome Research Institute (NHGRI)](https://www.genome.gov/), [Kent and Elizabeth Dauten Foundation](https://dautenbipolarcenter.org/about/dauten-family), and the [Dalio Foundation](https://www.daliophilanthropies.org/initiatives/mental-health-and-wellness/). The [contributing groups](/about) and the [terms of use](/terms) are listed on separate pages.
 
 Exome results browser last updated September 10th, 2020.

src/browsers/schema/content/terms.md

@@ -4,8 +4,8 @@ title: Terms of Use
 
 All data here are released under a [Fort Lauderdale Agreement](https://www.genome.gov/Pages/Research/WellcomeReport0303.pdf) for the benefit of the wider biomedical community for use in the investigation of the genetic causes of schizophrenia and, more generally, medical genetics research. Data and results may not be used in attempts to identify individual study participants. You can freely browse the case-control results; however, we ask that you not publish global (exome-wide) analyses of these data, or analyses of large gene sets, until after an initial schizophrenia exome meta-analysis paper has been published (estimated to be in Spring 2020). We encourage broad use of the frequency reference data but note that case-control results are provided as general guides and specific results may not have yet been subjected to the data quality, statistical and population genetics review that would normally be required for publication or clinical inference.
 
-If you are uncertain which category your analysis falls into, please [contact us](mailto:schema-questions@broadinstitute.org).
+If you are uncertain which category your analysis falls into, please [contact us](mailto:schema-inquiries@broadinstitute.org).
 
 ## Citations in publications
 
-We request that any use of data obtained from the SCHEMA browser cite the SCHEMA flagship paper and any online resources that include the data set provide a link to the browser.  
+We request that any use of data from the SCHEMA browser cite the consortium's flagship paper, and any online resources that include the data set provide a link to the browser.