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dbPEX – PEX-genendatabase  

Missie

Door genetische variaties te catalogiseren die betrokken zijn bij peroxisomale assemblageziekten, hopen we de analyse van deze variaties te versnellen en hun rol in gezondheid en ziekte beter te begrijpen.

PEX1: (peroxisomale biogenesefactor 1)

Algemene informatie over PEX1
Veld
Inhoud
Gensymbool PEX1
Gennaam peroxisomale biogenesefactor 1
Chromosoom 7
Chromosomale band q21.2
Genetische imprinting Onbekend
Genomische referentie NG_008341.2
Transcriptreferentie NM_000466.2
Geassocieerd met ziekten HMLR1, ID, PBD1A, PBD1B
Totaal aantal publieke varianten 932
Unieke publieke DNA-varianten 257
Individuen met publieke varianten 602
Verborgen varianten

31

PEX2: (peroxisomale biogenesefactor 2)

Algemene informatie over PEX2
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Gensymbool PEX2
Gennaam peroxisomale biogenesefactor 2
Chromosoom 8
Chromosomale band q21.11
Genetische imprinting Onbekend
Genomische referentie NG_008371.1
Transcriptreferentie NM_000318.2
Geassocieerd met ziekten PBD5A, PBD5B
Totaal aantal publieke varianten 67
Unieke publieke DNA-varianten 46
Individuen met publieke varianten 38
Verborgen varianten 4

PEX3: (peroxisomale biogenesefactor 3)

Algemene informatie over PEX3
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Gensymbool PEX3
Gennaam peroxisomale biogenesefactor 3
Chromosoom 6
Chromosomale band q24.2
Genetische imprinting Onbekend
Genomische referentie NG_008459.1
Transcriptreferentie NM_003630.2
Geassocieerd met ziekten PBD10A, PBD10B
Totaal aantal publieke varianten 21
Unieke publieke DNA-varianten 21
Individuen met publieke varianten 8
Verborgen varianten

PEX5: (peroxisomale biogenesefactor 5)

Algemene informatie over PEX5
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Gensymbool PEX5
Gennaam peroxisomale biogenesefactor 5
Chromosoom 12
Chromosomale band p
Genetische imprinting Onbekend
Genomische referentie NG_008448.1
Transcriptreferentie NM_000319.4
Geassocieerd met ziekten , PBD2A, PBD2B, RCDP5
Totaal aantal publieke varianten 65
Unieke publieke DNA-varianten 52
Individuen met publieke varianten 178
Verborgen varianten 7

PEX6: (peroxisomale biogenesefactor 6)

Algemene informatie over PEX6
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Gensymbool PEX6
Gennaam peroxisomale biogenesefactor 6
Chromosoom 6
Chromosomale band p22–p11
Genetische imprinting Onbekend
Genomische referentie NG_008370.1
Transcriptreferentie NM_000287.3
Geassocieerd met ziekten HMLR2, PBD4A, PBD4B
Totaal aantal publieke varianten 329
Unieke publieke DNA-varianten 211
Individuen met publieke varianten 340
Verborgen varianten 9

PEX7: (peroxisomale biogenesefactor 7)

Algemene informatie over PEX7
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Gensymbool PEX7
Gennaam peroxisomale biogenesefactor 7
Chromosoom 6
Chromosomale band q21–q22.2
Genetische imprinting Onbekend
Genomische referentie NG_008462.1
Transcriptreferentie NM_000288.3
Geassocieerd met ziekten ID, PBD9B, RCDP1, Refsum
Totaal aantal publieke varianten 294
Unieke publieke DNA-varianten 98
Individuen met publieke varianten 172
Verborgen varianten 11

PEX10: (peroxisomale biogenesefactor 10)

Algemene informatie over PEX10
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Gensymbool PEX10
Gennaam peroxisomale biogenesefactor 10
Chromosoom 1
Chromosomale band p36.32
Genetische imprinting Onbekend
Genomische referentie NG_008342.1
Transcriptreferentie NM_153818.1
Geassocieerd met ziekten ID, PBD6A, PBD6B
Totaal aantal publieke varianten 98
Unieke publieke DNA-varianten 65
Individuen met publieke varianten 41
Verborgen varianten 14

PEX12: (peroxisomale biogenesefactor 12)

Algemene informatie over PEX12
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Gensymbool PEX12
Gennaam peroxisomale biogenesefactor 12
Chromosoom 17
Chromosomale band q21.1
Genetische imprinting Onbekend
Genomische referentie NG_008447.1
Transcriptreferentie NM_000286.2
Geassocieerd met ziekten PBD3A, PDB3B
Totaal aantal publieke varianten 82
Unieke publieke DNA-varianten 44
Individuen met publieke varianten 59
Verborgen varianten -

PEX13: (peroxisomale biogenesefactor 13)

Algemene informatie over PEX13
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Gensymbool PEX13
Gennaam peroxisomale biogenesefactor 13
Chromosoom 2
Chromosomale band p16.1
Genetische imprinting Onbekend
Genomische referentie NG_008665.1
Transcriptreferentie NM_002618.3
Geassocieerd met ziekten ID, PBD11A, PBD11B
Totaal aantal publieke varianten 25
Unieke publieke DNA-varianten 23
Individuen met publieke varianten 11
Verborgen varianten 2

PEX14: (peroxisomale biogenesefactor 14)

Algemene informatie over PEX14
Veld Inhoud
Gensymbool PEX14
Gennaam peroxisomale biogenesefactor 14
Chromosoom 1
Chromosomale band p36.22
Genetische imprinting Onbekend
Genomische referentie NG_008340.2
Transcriptreferentie NM_004565.2
Geassocieerd met ziekten PBD13A
Totaal aantal publieke varianten 25
Unieke publieke DNA-varianten 24
Individuen met publieke varianten 48
Verborgen varianten 3

PEX16: (peroxisomale biogenesefactor 16)

Algemene informatie over PEX16
Veld Inhoud
Gensymbool PEX16
Gennaam peroxisomale biogenesefactor 16
Chromosoom 11
Chromosomale band p
Genetische imprinting Onbekend
Genomische referentie NG_008460.1
Transcriptreferentie NM_004813.2, , NM_057174.2
Geassocieerd met ziekten PBD8A, PBD8B
Totaal aantal publieke varianten 47
Unieke publieke DNA-varianten 37
Individuen met publieke varianten 134
Verborgen varianten 3

PEX19: (peroxisomale biogenesefactor 19)

Algemene informatie over PEX19
Veld Inhoud
Gensymbool PEX19
Gennaam peroxisomale biogenesefactor 19
Chromosoom 1
Chromosomale band q22
Genetische imprinting Onbekend
Genomische referentie NG_008637.1
Transcriptreferentie NM_002857.3
Geassocieerd met ziekten PBD12A
Totaal aantal publieke varianten 45
Unieke publieke DNA-varianten 38
Individuen met publieke varianten 7
Verborgen varianten 6

PEX26: (peroxisomale biogenesefactor 26)

Algemene informatie over PEX26
Veld Inhoud
Gensymbool PEX26
Gennaam peroxisomale biogenesefactor 26
Chromosoom 22
Chromosomale band q11.21
Genetische imprinting Onbekend
Genomische referentie NG_008339.1
Transcriptreferentie NM_017929.5
Geassocieerd met ziekten ID, PBD7A, PBD7B
Totaal aantal publieke varianten 83
Unieke publieke DNA-varianten 47
Individuen met publieke varianten 60
Verborgen varianten 6

Data Submission and Sharing:

Researchers can submit their findings on DNA-binding proteins to the platform, contributing to a growing body of knowledge that is accessible to the scientific community.

The platform may support various data formats, including sequence data, structural models, and experimental annotations


Analytical Tools and Resources:

Prediction Tools: Computational tools for predicting DNA-binding domains in proteins, identifying potential DNA-binding sites, and modeling protein-DNA interactions.

Visualization Tools: Features for visualizing protein-DNA complexes, allowing researchers to explore the structural details of these interactions in 3D.

Sequence Alignment and Analysis: Tools for comparing DNA-binding proteins across different species, identifying conserved motifs, and analyzing evolutionary relationships.

Research and Publications:


Access to a collection of research papers, reviews, and case studies focused on DNA-binding proteins. This may include articles on the discovery of new DBPs, studies on their role in various cellular processes, and advances in the technology used to study them.

The platform might also highlight key publications that have utilized data, demonstrating the impact and relevance of the resource in scientific research.


Collaboration and Community:


A platform for connecting researchers working on DNA-binding proteins, facilitating collaboration, data sharing, and the exchange of ideas.

Forums or discussion groups where users can ask questions, share insights, and discuss recent developments in the field of DNA-binding proteins.

Educational Resources:

Tutorials, webinars, and guides on using the database and associated tools, as well as educational content on DNA-binding proteins, their functions, and methods for studying them.

Resources designed to support both novice researchers and experienced scientists in making the most of the platform's offerings.

Application Areas:


The data and tools available on DBPEx.g are relevant to a wide range of biological and medical research areas, including gene regulation, epigenetics, cancer research, and the development of novel therapeutics targeting DNA-protein interactions.

Use Cases:

Basic Research: Scientists studying the fundamental biology of DNA-binding proteins, their roles in gene expression, and their impact on cellular processes.

Drug Discovery: Researchers looking for potential targets in DNA-binding proteins for developing new drugs, especially in areas like oncology or infectious diseases.

Bioinformatics: Computational biologists who need access to datasets and tools for modeling protein-DNA interactions and predicting DNA-binding sites.



LOVD stands for Leiden Open (source) Variation Database. LOVD is designed to provide a flexible, freely available tool for gene-centered collection and display of DNA variations.

LOVD was developed approaching the "LSDB-in-a-Box" idea for the easy creation and maintenance of a fully web-based gene sequence variation database, that is platform-independent and uses PHP and MySQL open source software only. The basic gene-centered and modular design of the database follows the recommendations of the Human Genome Variation Society (HGVS) and focuses on the collection and display of the DNA sequence variations but it is extendable with clinical data with minimal effort. The open LOVD set up also facilitates functional extensions with scripts written by the community.

The development of (then nameless) LOVD started in late 2002, while it was first officially released in January, 2004. Before that LOVD was only in use by the Leiden Muscular Dystrophy pages, as a not-so-modular system with lots of characteristics specific for that website only. With the official release of LOVD in 2004 the system had become much more dynamic and customizing LOVD was made easy mostly by editing text-files.

In 2004, LOVD became available under the open source license GPL and with the 1.1.0 release most of the text-files had been replaced by online forms so customisations can be performed through the web interface. Early in 2005 the LOVD article was published, and in 2005 the development of LOVD was more targeted at improving the ease of use of the system.

In 2006 the development of LOVD 2.0 started after the decision was made to rewrite all of LOVD from scratch to be able to include a long list of upgrade suggestions that were hard to implement in LOVD 1.1.0. Aimed at modularity and data redundancy, LOVD 2.0 was meant to be a more flexible and more powerful successor of the popular 1.1.0 version and soon it received the interest of LOVD users eager to try out the all-new version.

LOVD 2.0 reached alpha stage in November 2006 after which a select group of enthusiastic LOVD users started testing the database software. With more features being added and bugs fixed rapidly, LOVD 2.0 reached beta stage in April 2007, after which more and more users started to upgrade their 1.1.0 databases to 2.0. Finally, in October 2007 LOVD 2.0 reached the stable stage but even now LOVD 2.0 is continuously improved. Every last Friday of the month, a new release is available from the LOVD website.