LIVIVO - Search results -

Search results

Result 1 - 10 of total 86

Search options

Article ; Online: Cluster Analysis of Short Sensory Profile Data Reveals Sensory-Based Subgroups in Autism Spectrum Disorder

Ariel M. Lyons-Warren / Michael F. Wangler / Ying-Wooi Wan

International Journal of Molecular Sciences, Vol 23, Iss 13030, p

2022 Volume 13030

Abstract: Autism spectrum disorder is a common, heterogeneous neurodevelopmental disorder lacking targeted treatments. Additional features include restricted, repetitive patterns of behaviors and differences in sensory processing. We hypothesized that detailed ... ...

Abstract	Autism spectrum disorder is a common, heterogeneous neurodevelopmental disorder lacking targeted treatments. Additional features include restricted, repetitive patterns of behaviors and differences in sensory processing. We hypothesized that detailed sensory features including modality specific hyper- and hypo-sensitivity could be used to identify clinically recognizable subgroups with unique underlying gene variants. Participants included 378 individuals with a clinical diagnosis of autism spectrum disorder who contributed Short Sensory Profile data assessing the frequency of sensory behaviors and whole genome sequencing results to the Autism Speaks’ MSSNG database. Sensory phenotypes in this cohort were not randomly distributed with 10 patterns describing 43% (162/378) of participants. Cross comparison of two independent cluster analyses on sensory responses identified six distinct sensory-based subgroups. We then characterized subgroups by calculating the percent of patients in each subgroup who had variants with a Combined Annotation Dependent Depletion (CADD) score of 15 or greater in each of 24,896 genes. Each subgroup exhibited a unique pattern of genes with a high frequency of variants. These results support the use of sensory features to identify autism spectrum disorder subgroups with shared genetic variants.
Keywords	neurodevelopmental disorders ; human genetics ; sensory processing ; autism spectrum disorder ; phenotypic biomarker ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Language	English
Publishing date	2022-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: CoRegNet: unraveling gene co-regulation networks from public RNA-Seq repositories using a beta-binomial statistical model.

Wang, Jiasheng / Wan, Ying-Wooi / Al-Ouran, Rami / Huang, Meichen / Liu, Zhandong

Briefings in bioinformatics

2023 Volume 25, Issue 1

Abstract: Millions of RNA sequencing samples have been deposited into public databases, providing a rich resource for biological research. These datasets encompass tens of thousands of experiments and offer comprehensive insights into human cellular regulation. ... ...

Abstract	Millions of RNA sequencing samples have been deposited into public databases, providing a rich resource for biological research. These datasets encompass tens of thousands of experiments and offer comprehensive insights into human cellular regulation. However, a major challenge is how to integrate these experiments that acquired at different conditions. We propose a new statistical tool based on beta-binomial distributions that can construct robust gene co-regulation network (CoRegNet) across tens of thousands of experiments. Our analysis of over 12 000 experiments involving human tissues and cells shows that CoRegNet significantly outperforms existing gene co-expression-based methods. Although the majority of the genes are linearly co-regulated, we did discover an interesting set of genes that are non-linearly co-regulated; half of the time they change in the same direction and the other half they change in the opposite direction. Additionally, we identified a set of gene pairs that follows the Simpson's paradox. By utilizing public domain data, CoRegNet offers a powerful approach for identifying functionally related gene pairs, thereby revealing new biological insights.
MeSH term(s)	Humans ; RNA-Seq ; Gene Regulatory Networks ; Models, Statistical ; Sequence Analysis, RNA/methods ; Gene Expression Profiling/methods
Language	English
Publishing date	2023-12-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbad380
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6262: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Cluster Analysis of Short Sensory Profile Data Reveals Sensory-Based Subgroups in Autism Spectrum Disorder.

Lyons-Warren, Ariel M / Wangler, Michael F / Wan, Ying-Wooi

International journal of molecular sciences

2022 Volume 23, Issue 21

Abstract	Autism spectrum disorder is a common, heterogeneous neurodevelopmental disorder lacking targeted treatments. Additional features include restricted, repetitive patterns of behaviors and differences in sensory processing. We hypothesized that detailed sensory features including modality specific hyper- and hypo-sensitivity could be used to identify clinically recognizable subgroups with unique underlying gene variants. Participants included 378 individuals with a clinical diagnosis of autism spectrum disorder who contributed Short Sensory Profile data assessing the frequency of sensory behaviors and whole genome sequencing results to the Autism Speaks' MSSNG database. Sensory phenotypes in this cohort were not randomly distributed with 10 patterns describing 43% (162/378) of participants. Cross comparison of two independent cluster analyses on sensory responses identified six distinct sensory-based subgroups. We then characterized subgroups by calculating the percent of patients in each subgroup who had variants with a Combined Annotation Dependent Depletion (CADD) score of 15 or greater in each of 24,896 genes. Each subgroup exhibited a unique pattern of genes with a high frequency of variants. These results support the use of sensory features to identify autism spectrum disorder subgroups with shared genetic variants.
MeSH term(s)	Humans ; Autism Spectrum Disorder/genetics ; Autistic Disorder/genetics ; Phenotype ; Cluster Analysis ; Cohort Studies
Language	English
Publishing date	2022-10-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms232113030
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: MicroRNA, mRNA, and Proteomics Biomarkers and Therapeutic Targets for Improving Lung Cancer Treatment Outcomes.

Ye, Qing / Raese, Rebecca / Luo, Dajie / Cao, Shu / Wan, Ying-Wooi / Qian, Yong / Guo, Nancy Lan

Cancers

2023 Volume 15, Issue 8

Abstract: The majority of lung cancer patients are diagnosed with metastatic disease. This study identified a set of 73 microRNAs (miRNAs) that classified lung cancer tumors from normal lung tissues with an overall accuracy of 96.3% in the training patient cohort ( ...

Abstract	The majority of lung cancer patients are diagnosed with metastatic disease. This study identified a set of 73 microRNAs (miRNAs) that classified lung cancer tumors from normal lung tissues with an overall accuracy of 96.3% in the training patient cohort (
Language	English
Publishing date	2023-04-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers15082294
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: MeCP2 regulates

Bajikar, Sameer S / Anderson, Ashley G / Zhou, Jian / Durham, Mark A / Trostle, Alexander J / Wan, Ying-Wooi / Liu, Zhandong / Zoghbi, Huda Y

eLife

2023 Volume 12

Abstract: Loss- and gain-of-function of MeCP2 causes Rett syndrome (RTT) ... ...

Abstract	Loss- and gain-of-function of MeCP2 causes Rett syndrome (RTT) and
MeSH term(s)	Animals ; Mice ; Rett Syndrome ; Nervous System Physiological Phenomena ; Aging ; Disease Models, Animal ; Growth Differentiation Factors/genetics ; Bone Morphogenetic Proteins/genetics ; Methyl-CpG-Binding Protein 2/genetics
Chemical Substances	Growth Differentiation Factors ; Gdf11 protein, mouse ; Bone Morphogenetic Proteins ; Mecp2 protein, mouse ; Methyl-CpG-Binding Protein 2
Language	English
Publishing date	2023-02-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.83806
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: A Comprehensive and Integrative Approach to MeCP2 Disease Transcriptomics.

Trostle, Alexander J / Li, Lucian / Kim, Seon-Young / Wang, Jiasheng / Al-Ouran, Rami / Yalamanchili, Hari Krishna / Liu, Zhandong / Wan, Ying-Wooi

International journal of molecular sciences

2023 Volume 24, Issue 6

Abstract: Mutations in MeCP2 result in a crippling neurological disease, but we lack a lucid picture of MeCP2's molecular role. Individual transcriptomic studies yield inconsistent differentially expressed genes. To overcome these issues, we demonstrate a ... ...

Abstract	Mutations in MeCP2 result in a crippling neurological disease, but we lack a lucid picture of MeCP2's molecular role. Individual transcriptomic studies yield inconsistent differentially expressed genes. To overcome these issues, we demonstrate a methodology to analyze all modern public data. We obtained relevant raw public transcriptomic data from GEO and ENA, then homogeneously processed it (QC, alignment to reference, differential expression analysis). We present a web portal to interactively access the mouse data, and we discovered a commonly perturbed core set of genes that transcends the limitations of any individual study. We then found functionally distinct, consistently up- and downregulated subsets within these genes and some bias to their location. We present this common core of genes as well as focused cores for up, down, cell fraction models, and some tissues. We observed enrichment for this mouse core in other species MeCP2 models and observed overlap with ASD models. By integrating and examining transcriptomic data at scale, we have uncovered the true picture of this dysregulation. The vast scale of these data enables us to analyze signal-to-noise, evaluate a molecular signature in an unbiased manner, and demonstrate a framework for future disease focused informatics work.
MeSH term(s)	Mice ; Animals ; Rett Syndrome/genetics ; Transcriptome ; Methyl-CpG-Binding Protein 2/genetics ; Methyl-CpG-Binding Protein 2/metabolism ; Gene Expression Profiling ; Mutation ; Disease Models, Animal
Chemical Substances	Methyl-CpG-Binding Protein 2 ; Mecp2 protein, mouse
Language	English
Publishing date	2023-03-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24065122
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: MATR3 pathogenic variants differentially impair its cryptic splicing repression function.

Khan, Mashiat / Chen, Xiao Xiao Lily / Dias, Michelle / Santos, Jhune Rizsan / Kour, Sukhleen / You, Justin / van Bruggen, Rebekah / Youssef, Mohieldin M M / Wan, Ying-Wooi / Liu, Zhandong / Rosenfeld, Jill A / Tan, Qiumin / Pandey, Udai Bhan / Yalamanchili, Hari Krishna / Park, Jeehye

FEBS letters

2024 Volume 598, Issue 4, Page(s) 415–436

Abstract: Matrin-3 (MATR3) is an RNA-binding protein implicated in neurodegenerative and neurodevelopmental diseases. However, little is known regarding the role of MATR3 in cryptic splicing within the context of functional genes and how disease-associated ... ...

Abstract	Matrin-3 (MATR3) is an RNA-binding protein implicated in neurodegenerative and neurodevelopmental diseases. However, little is known regarding the role of MATR3 in cryptic splicing within the context of functional genes and how disease-associated variants impact this function. We show that loss of MATR3 leads to cryptic exon inclusion in many transcripts. We reveal that ALS-linked S85C pathogenic variant reduces MATR3 solubility but does not impair RNA binding. In parallel, we report a novel neurodevelopmental disease-associated M548T variant, located in the RRM2 domain, which reduces protein solubility and impairs RNA binding and cryptic splicing repression functions of MATR3. Altogether, our research identifies cryptic events within functional genes and demonstrates how disease-associated variants impact MATR3 cryptic splicing repression function.
MeSH term(s)	Humans ; Amyotrophic Lateral Sclerosis/genetics ; Exons/genetics ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; RNA ; Nuclear Matrix-Associated Proteins/genetics
Chemical Substances	RNA-Binding Proteins ; RNA (63231-63-0) ; MATR3 protein, human ; Nuclear Matrix-Associated Proteins
Language	English
Publishing date	2024-02-06
Publishing country	England
Document type	Journal Article
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.14806
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.B 282: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Disruption of the ATXN1-CIC complex reveals the role of additional nuclear ATXN1 interactors in spinocerebellar ataxia type 1.

Coffin, Stephanie L / Durham, Mark A / Nitschke, Larissa / Xhako, Eder / Brown, Amanda M / Revelli, Jean-Pierre / Villavicencio Gonzalez, Esmeralda / Lin, Tao / Handler, Hillary P / Dai, Yanwan / Trostle, Alexander J / Wan, Ying-Wooi / Liu, Zhandong / Sillitoe, Roy V / Orr, Harry T / Zoghbi, Huda Y

Neuron

2023 Volume 111, Issue 6, Page(s) 915

Language	English
Publishing date	2023-03-15
Publishing country	United States
Document type	Published Erratum
ZDB-ID	808167-0
ISSN	1097-4199 ; 0896-6273
ISSN (online)	1097-4199
ISSN	0896-6273
DOI	10.1016/j.neuron.2023.02.030
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2496: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 92: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: MeCP2 regulates Gdf11, a dosage-sensitive gene critical for neurological function

Sameer S Bajikar / Ashley G Anderson / Jian Zhou / Mark A Durham / Alexander J Trostle / Ying-Wooi Wan / Zhandong Liu / Huda Y Zoghbi

eLife, Vol

2023 Volume 12

Abstract: Loss- and gain-of-function of MeCP2 causes Rett syndrome (RTT) and MECP2 duplication syndrome (MDS), respectively. MeCP2 binds methyl-cytosines to finely tune gene expression in the brain, but identifying genes robustly regulated by MeCP2 has been ... ...

Abstract	Loss- and gain-of-function of MeCP2 causes Rett syndrome (RTT) and MECP2 duplication syndrome (MDS), respectively. MeCP2 binds methyl-cytosines to finely tune gene expression in the brain, but identifying genes robustly regulated by MeCP2 has been difficult. By integrating multiple transcriptomics datasets, we revealed that MeCP2 finely regulates growth differentiation factor 11 (Gdf11). Gdf11 is down-regulated in RTT mouse models and, conversely, up-regulated in MDS mouse models. Strikingly, genetically normalizing Gdf11 dosage levels improved several behavioral deficits in a mouse model of MDS. Next, we discovered that losing one copy of Gdf11 alone was sufficient to cause multiple neurobehavioral deficits in mice, most notably hyperactivity and decreased learning and memory. This decrease in learning and memory was not due to changes in proliferation or numbers of progenitor cells in the hippocampus. Lastly, loss of one copy of Gdf11 decreased survival in mice, corroborating its putative role in aging. Our data demonstrate that Gdf11 dosage is important for brain function.
Keywords	growth differentiation factor 11 ; Methyl CpG Binding Protein 2 ; MECP2 duplication syndrome ; GDF11 ; MeCP2 ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: A Comprehensive and Integrative Approach to MeCP2 Disease Transcriptomics

Alexander J. Trostle / Lucian Li / Seon-Young Kim / Jiasheng Wang / Rami Al-Ouran / Hari Krishna Yalamanchili / Zhandong Liu / Ying-Wooi Wan

International Journal of Molecular Sciences, Vol 24, Iss 5122, p

2023 Volume 5122

Abstract: Mutations in MeCP2 result in a crippling neurological disease, but we lack a lucid picture of MeCP2′s molecular role. Individual transcriptomic studies yield inconsistent differentially expressed genes. To overcome these issues, we demonstrate a ... ...

Abstract	Mutations in MeCP2 result in a crippling neurological disease, but we lack a lucid picture of MeCP2′s molecular role. Individual transcriptomic studies yield inconsistent differentially expressed genes. To overcome these issues, we demonstrate a methodology to analyze all modern public data. We obtained relevant raw public transcriptomic data from GEO and ENA, then homogeneously processed it (QC, alignment to reference, differential expression analysis). We present a web portal to interactively access the mouse data, and we discovered a commonly perturbed core set of genes that transcends the limitations of any individual study. We then found functionally distinct, consistently up- and downregulated subsets within these genes and some bias to their location. We present this common core of genes as well as focused cores for up, down, cell fraction models, and some tissues. We observed enrichment for this mouse core in other species MeCP2 models and observed overlap with ASD models. By integrating and examining transcriptomic data at scale, we have uncovered the true picture of this dysregulation. The vast scale of these data enables us to analyze signal-to-noise, evaluate a molecular signature in an unbiased manner, and demonstrate a framework for future disease focused informatics work.
Keywords	MeCP2 ; data portal ; Rett syndrome ; MeCP2 duplication syndrome ; RNA-seq ; differential expression analysis ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	612
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED