Tag: cell biology

The Human Protein Atlas is program started with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies. It consists of three parts: Tissue Atlas showing the distribution of proteins acros ...

The Database of Protein Disorder (DisProt) is a curated database that provides information about intrinsically disordered proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Disordered regions ...

A database of exosomes, membrane vesicles of endocytic origin released by diverse cell types.

The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines w ...

Useful biological numbers

APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome ...

FuzDB compiles experimentally observed fuzzy protein complexes, where intrinsic disorder (ID) is maintained upon interacting with a partner (protein, nucleic acid or small molecule) and directly impacts biological function. Entries in the database ha ...

Aniseed is a database designed to offer a representation of ascidian embryonic development at the level of the genome (cis-regulatory sequences, spatial gene expression, protein annotation), of the cell (cell shapes, fate, lineage) or of the whole em ...

HIstome (Human histone database) is a freely available, specialist, electronic database dedicated to display information about human histone variants, sites of their post-translational modifications and about various histone modifying enzymes.

PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other path ...

The human pluripotent stem cell registry (hPSCreg) is a public registry and data portal for human embryonic and induced pluripotent stem cell lines (hESC and hiPSC). The Registry provides comprehensive and standardized biological and legal informatio ...

Spatially resolved transcriptomics providing gene expression profiles with positional information is key to tissue function and fundamental to disease pathology. SpatialDB is the first public database that specifically curates spatially resolved tran ...

Mitochondrial genome database of fish with an accurate and automatic annotation pipeline.

COVDB contains cell culture, animal model, and clinical data on compounds with a proven or potential anti-coronavirus activity.

Metabolic gEne RApid Visualizer

To enable interoperability of genome annotations, we have developed the Genome Biology Ontology Language (GBOL) and associated stack (GBOL stack). GBOL is provenance centered and provides a consistent representation of genome derived automated predic ...

ADPriboDB is a database of ADP-ribosylated proteins and their literature-identified ADP-ribosylated residues. The database includes a variety of information for each entry, including any drug treatments performed to obtain the identification of the m ...

Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons. Enhancers, as well as their associated target genes, and transcription factors (TFs) that bind to them, a ...

ATCC authenticates microorganisms and cell lines and manages logistics of long-term preservation and distribution of cultures for the scientific community. ATCC supports the cultures it acquires and authenticates with expert technical support, intell ...

A comprehensive on-line resource with curated datasets of mitochondrial DNA (mtDNA) rearrangements.

GlycoPOST is a mass spectrometry data repository for glycomics. Users can release their "raw/processed" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information ...

Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid–liquid phase separation (LLPS), a process that relies on multiv ...

Recode2 is a database of genes that utilize non-standard translation for gene expression purposes. Recoding events described in the database include programmed ribosomal frameshifting, translational bypassing (aka hopping) and mRNA specific codon red ...

REFOLDdb is a resource for the optimization of protein refolding, referring to published methods employed in the refolding of recombinant proteins. It stores a collection of published experimental approaches and records for refolding proteins. It con ...

The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is an open-access, comprehensive database containing information on amino acid sequences, chemical modifications, 3D structures, bioactivities and toxicities of peptides that p ...

PhaSepDB is a novel database that provides a collection of phase separation related proteins manually curated from publications and public database. In addition to curated proteins, PhaSepDB also provides the researchers with molecular signatures th ...

A database for systems biology of DNA dynamics during the cell life.

A data resource of liquid-liquid phase separation in eukaryotes. Here, we presented a data resource of LLPS (DrLLPS), a comprehensive data resource that contained 437,887 known and computationally detected LLPS-associated proteins in 164 eukaryotic ...

a database of endothelial cell transcriptomics data. EndoDB The endothelial cell database (EndoDB) is a freely accessible added-value database that facilitates bench scientists to unlock the untapped potential of publicly available (single cell) tra ...

an interactive database of human snoRNA sequences, abundance and interactions. Tool to visualize expression data in heatmaps. Column Options Reset Filters Refresh Table. snoTHAW is a tool to help visualize snoRNA expression data from snoDB

RNA Localization in the cell

Cell type specificity of genetic traits

Searchable collection of biomedical books linked to terms in PubMed abstracts; when viewing an abstract, click on Books link to see phrases in abstract hyperlinked to book sections.

CellO (Cell Ontology-based classification) is a Python package for performing cell type classification of human RNA-seq data. CellO makes hierarchical predictions against the Cell Ontology. These classifiers were trained on nearly all of the human pr ...

Human IRES Atlas is an integrative platform for studying IRES-driven translational regulation in humans.

A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. PRESDB:pig RNA Editing database

Database of single-cell expression map across various human cancers.

A knowledgebase of cellular drug response.

PlanExp is an intuitive integration of complex RNA-seq datasets with planarian omics resources.

OGT Protein Interaction Network (OGT-PIN) is a curated and comprehensive database of experimentally identified interaction proteins of OGT and its orthologues in multiple species studied in the past several decades.

A comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels.

A comprehensive mitochondrial toxicity database.

The human Ensemble Cell Atlas (hECA) a database.

ColorCells is a database of expression, classification and functions of lncRNAs in single cells. Single cell RNA sequencing (scRNA-Seq) technology has revealed significant differences in gene expression levels between different cell groups.

The database provides single-cell enhancer annotation in three species, including human (hg19), mouse (mm9), and fly (dm3).

A comprehensive database of RNAs involved in liquid-liquid phase separation.

Functional annotation of the first artificial organism Mycoplasma mycoides JCVI-syn3A.

A dedicated database of non-B cell derived immunoglobulin variable region. Non-B cell derived ImmunoGlobulin Variable region Database. Welcome to NBIGV, a database dedicated to organizing and characterizing non-B cell derived immunoglobulins.

User-editable lineage maps illustrating both endogenous development and the directed differentiation of human and mouse embryonic stem cells.

A database of mitochondrial genome variants in chinese population

A host-pathogen interactome database for deciphering crucial molecular networks of wheat-common bunt cross-talk mechanisms.

A database of human tissue functional gene networks built with a large compendium of curated RNA-seq data.

DeepMitoDB is a database of experimental and predicted subcellular localization of mitochondrial proteins with exteded functional annotation.

RNAPhaSep is a novel database that collects phase separation related RNAs manually curated from publication and public databases. Various properties of RNAs together with the corresponding phase separation conditions validated by experiments were col ...

A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. The main web resource to explore human mitochondrial variability data and their pathological correlation. HmtVar is a manually-curate ...

DatumKB is a freely accessible database of experimental results involving the function and regulation of human proteins in cultured cells. The results are manually curated from biological research literature using a shorthand language and stored as d ...

A curated repository of cell types with multifaceted characterization.

This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The Cell Image Library has been merged with "Cell Centered Datab ...

A collection of genes and proteins involved in human and yeast cell cycle.

BioAssay Research Database

Biobanking Analysis Resource Catalogue

Data portal for standardized stem cell information. ICSCB is operated by CiRA,Kyoto University. It is an Intergerated Collection of Stem Cell Bank data by miacarm, standard data format for all the stem cell lines with minimum necessary information f ...

A curated and comprehensive resource of plant cell markers.

Cell line integrated molecular authentication.

Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data.

Clones and libraries: sequence data, map positions and distributor information

Predicted genome, proteome, and reactome of LUCA

Plant transfer RNA database.

The Swiss Portal for Immune Cell Analysis (SPICA) is a web resource dedicated to the exploration and analysis of single-cell RNA-seq data of immune cells.

Cloud-based platform to manage and share antibody-based single-cell research.

A database of nucleosome positioning in vivo and nucleosomics of cell-free DNA.

MycoWiki is organizes data under a relational database and provides access to curated and state-of-the-art information on the genes and proteins of M. pneumoniae.

A comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation.

A Functional Annotation Resource for Deciphering the Complete Interaction Networks in Wheat-Karnal Bunt Pathosystem.

rPanglaoDB is an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. A meta-analysis database for single cell RNA sequencing data. Search across datasets, studies, download data, and perform advanced visualiz ...

A web-based application for detecting microbial contaminants in next-generation sequencing data. OpenContami: Open Cell Microbial Contaminants by High-throughput Sequencing.

Database which collects human and mouse embryonic stem cell related datasets. These datasets cover perturbation (both knock-down and overexpression) and chromatin immunoprecipitation (ChIP) experiments in embryonic stem (ES) and carcinoma (EC) cell l ...

PIDE (Particle Irradiation Data Ensemble) is a radiobiological database compiling more than 1100 pairs of in-vitro cell survival experiments after photon and ion irradiation.

A knowledgebase and transparency tool for minimum information in spheroid identity.

Pathway analysis database of drug response based on phosphorylation activity measurements.

A webtool to identify and analyze bacterial microcompartment types in sequence data.

ProModb (Protein interaction-based functional Module database) is a repository that documents computationally generated whole-cell protein-protein interaction network-based functional modules of an organism.

A Database and User Interface for scRNA-seq Marker Genes.

An integrative database of diseases related variations in liquid-liquid phase separation proteins.

MitopatHs is a database that allows to navigate among the biochemical pathways (PatHs) of human (H) mitochondria (Mito). It is a logically-framed tool for visualizing multiple mitochondrial pathways.

A knowledge database of dense granule proteins of the Apicomplexa.

CFM is a database of experimentally validated protocols for chemical compound-based direct reprogramming and transdifferentiation.

A comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human.

An online tool for designing highly efficient sgRNAs targeting cell surface proteins

CoDNaS Quaternary is a high confidence database of conformational diversity in proteins that present a biologically relevant quaternary structure.

Culture collection of algae and protozoa.

A database and web application for analyzing embryonic stem cells differentiation process on mouse model. The data is collected by FunGenES consortium and organized into six clusters to facilitate data mining.

Accurate Prediction of Kinase-Substrate Networks Using Knowledge Graphs. Abstract Phosphorylation of specific substrates by protein kinases is a key control mechanism for vital cell-fate decisions and other cellular processes. However, discovering s ...

A web database for sequence and shape motif analyses and identification.

Limonada (Lipid Membrane Open Network And Database) is a database dedicated to the simulation of biological membranes. limonada intends to provide an open library of membranes, along with the description of lipids, topologies and forcefields mandato ...

>>>!!!<<< 2021-08; The repository is no longer available. >>>!!!<<< Archived page of Taenia solium genome project see https://web.archive.org/web/20160309194611/http://www.taeniasolium.unam.mx/taenia

A comprehensive organelle genomes database for algae cpDNA and mtDNA. Algae is the earliest evolutionary biological group on the earth, are thought to have appeared at least 2.6 billion years ago. As the most complex biological group, algae have sho ...

Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products. decRiPPter (Data-driven Exploratory Class-independent RiPP TrackER). Alexander M. Kloosterman, Peter Cimermancic, Somayah S. Elsayed, Chao ...

The Bacterial Microcompartment Database. MCPdb – The Bacterial Microcompartment Databse. MCPDB A bacterial microcompartment database and structure viewer include Carboxysome Pdu Eut BMC BMV MCP organelle encapsulin protein capsid. MCPdb is an onli ...