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Links tagged with 'micrornas'

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Found 38 links

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AHD2.0Database Content

http://ahd.cbi.pku.edu.cn/

Model Organisms > Databases

Arabidopsis Hormone Database (AHD) is a collection of hormone related genes of the model organism Arabidopsis thaliana (AHRGs). AHD2.0 has new features: (i) updating our collection of AHRGs based on most recent publications as well as constructing elaborate schematic diagrams of each hormone biosynthesis and signaling pathways; (ii) adding orthologs of sequenced plants listed in OrthoMCL-DB to each AHRG in the updated database; (iii) providing predicted miRNA splicing site(s) for each AHRG; (iv) integrating genes that genetically interact with each AHRG according to literatures mining; (v) providing links to a powerful online analysis platform WebLab for the convenience of in-time bioinformatics analysis and (vi) providing links to widely used protein databases and integrating more expression profiling information that would facilitate users for a more systematic and integrative analysis related to phytohormone research.

NAR Database Issue 2011
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tagsarabidopsis genetic databases micrornas plant genes plant growth regulators rna splicing

CrossLinkTool Content

http://www-ab.informatik.uni-tuebingen.de/software/crosslink/webstart/welcome.ht...

RNA > Functional RNAs
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Crosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. CrossLink can be useful for investigating potential interactions between microRNAs and their targets.

NAR Web Server Issue 2006
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tagsmicrornas rna sequence analysis sequence alignment

CRSDDatabase Content

http://140.120.213.10:8080/crsd/main/home.jsp

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
RNA > Functional RNAs

Composite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).

NAR Web Server Issue 2006
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tags3' untranslated regions binding sites cluster analysis gene expression profiling gene expression regulation genetic databases genetic promoter regions genomics humans micrornas oligonucleotide array sequence analysis transcription factors

DIANA-microTTool Content

http://www.microrna.gr/microT

Expression > Gene Regulation
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Worm
RNA > Functional RNAs

The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser.

NAR Web Server Issue 2009NAR Web Server Issue 2011
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tagsalgorithms binding sites gene expression regulation messenger rna micrornas rna sequence analysis

DroIDDatabase Content

http://droidb.org/

DNA > Databases
Model Organisms > Databases
Protein > Databases

DroID, the Drosophila Interactions Database, is a comprehensive public resource for Drosophila gene and protein interactions. DroID contains genetic interactions and experimentally detected protein-protein interactions curated from the literature and from external databases, and predicted protein interactions based on experiments in other species. Protein interactions are annotated with experimental details and periodically updated confidence scores. The database now includes transcription factor-gene and regulatory RNA-gene interactions. Orthologous gene mappings of Drosophila genes to other organisms are also available to facilitate finding interactions based on gene names and identifiers for a number of common model organisms and humans.

NAR Database Issue 2011
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tagsanimals drosophila drosophila proteins gene expression gene regulatory networks genetic databases insect genes micrornas protein interaction mapping systems integration transcription factors

DSAPTool Content

http://dsap.cgu.edu.tw

Expression > Transcript Expression Analysis
RNA > Functional RNAs

Deep-Sequencing Small RNA Analysis Pipeline (DSAP) is an automated web service designed to provide analysis of deep sequencing small RNA datasets from the Solexa sequencing platform. Non-coding RNA and miRNA matching are output based on homology mapping to Rfam and miRBase databases.

NAR Web Server Issue 2010
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tagsmicrornas rna sequence analysis untranslated rna

GeneCodisTool Content

http://genecodis.dacya.ucm.es

Computer Related > Web Services
DNA > Annotations
Expression > Gene Set Analysis
Expression > Networks

Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations.

NAR Web Server Issue 2009
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tagsanimals cattle gene expression regulation genes humans mice micrornas rats systems integration transcription factors

GeneSet2miRNATool Content

http://mips.helmholtz-muenchen.de/proj/gene2mir/

Expression > Gene Regulation
Expression > Gene Set Analysis

GeneSet2miRNA is a web based tool for identification of miRNA regulatory activity within an input gene list. A list of miRNA regulatory models is output.

NAR Web Server Issue 2009
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tagsanimals gene expression regulation genes humans mice micrornas rats

GenomeTraFaCTool Content

http://genometrafac.cchmc.org/genome-trafac/index.jsp

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

GenomeTraFaC is a comparative genomics based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq gene orthologs.

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tagsanimals base sequence binding sites conserved sequence genomics humans mice micrornas nucleic acid databases transcription factors transcriptional regulatory elements

HLungDBDatabase Content

http://www.megabionet.org/bio/hlung/

Human Genome > Databases

The human lung cancer database (HLungDB) is a database with the integration of the lung cancer-related genes, proteins and miRNAs together with the corresponding clinical information. Currently, we have collected 2585 genes and 212 miRNA with the experimental evidences involved in the different stages of lung carcinogenesis through text mining. The results from analysis of transcription factor-binding motifs, the promoters and the SNP sites for each gene are also included. Genes with epigenetic regulation were also included.

NAR Database Issue 2010
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tagsamino acid motifs computational biology gene regulatory networks genetic databases genetic epigenesis humans lung neoplasms micrornas neoplastic cell transformation nucleic acid databases protein databases transcription factors

MAGIATool Content

http://gencomp.bio.unipd.it/magia

Expression > Gene Set Analysis
Expression > Transcript Expression Analysis
RNA > Functional RNAs

miRNA and Genes Integrated Analysis (MAGIA) is a web tool for the integrative analysis of target predictions, miRNA and gene expression data

NAR Web Server Issue 2010
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tagsgene expression gene expression profiling gene regulatory networks humans messenger rna micrornas

mESAdbDatabase Content

http://konulab.fen.bilkent.edu.tr/mirna/

RNA > Databases

microRNA expression and sequence analysis database (mESAdb) is a database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO.

NAR Database Issue 2011
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tagsanimals humans mice micrornas nucleic acid databases rna sequence analysis systems integration

MicroInspectorTool Content

http://bioinfo.uni-plovdiv.bg/microinspector/

Expression > Gene Regulation
RNA > Functional RNAs
RNA > Motifs

MicroInspector is a tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites.

NAR Web Server Issue 2005
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tagsbase pairing binding sites messenger rna micrornas rna sequence analysis

miPredTool Content

http://www.bioinf.seu.edu.cn/miRNA/

RNA > Functional RNAs

miPred (microRNA Predictor) can distinguish between real and pseudo microRNA precursors.

NAR Web Server Issue 2007
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tagsanimals base sequence computational biology computer simulation false positive reactions genome genomics humans messenger rna micrornas molecular sequence data nucleic acid conformation species specificity

MIPSDatabase Content

http://mips.helmholtz-muenchen.de

Protein > Databases

The Munich Information Center for Protein Sequences (MIPS) provides annotated collections of biological data. High-quality reference resources include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis.

NAR Database Issue 2011
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tagsdata mining genetic databases genomics metabolomics micrornas neoplasm genes phenotype plant genome protein databases protein sequence analysis proteomics systems integration