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About Phenomir

The aim of this resource is to provide information about the relation between a disease/phenotype and the expression of miRNAs. In addition, PhenomiR offers information about the general conditions of the studies (study design), e.g. in vitro study or patients versus healthy persons, the experimental setup and miRNA target genes.

GENERAL INFORMATION


Database-ID
Each entry gets an unique database-id. An entry is based on the PMID of a scientific article and a disease or a biological process. If e.g. more than one disease is analyzed in an article, one entry is generated for each disease. The same is true if there are differences in the type of analysis, e.g. if cell cultures as well as patient samples are analyzed.

PMID
PubMed ID of the annotated article.

Bioprocess
In addition to diseases, PhenomiR provides information about differential miRNA expression in biological processes like organ development. If possible these processes are annotated using GO terms.

Disease
The name of the disease is annotated using an OMIM term or, if no appropriate term exists in OMIM, one of the 22 disease classes which was introduced by Goh et al. (Goh et al., PNAS, 2007, 104(21):8685-90) is used. Disease int.: If a disease or general term of a disease (like Thyroid carcinoma) is not available in the OMIM list, it is introduced. If a disease, a more general term of a disease or subtypes of a disease are not available in the OMIM list, it is introduced. Comment: For additional information concerning a disease or bioprocess a comment field is available.

STUDY INFORMATION


Study design
The field provides information about the general design of the study. The following terms are available: -Patient study control -phenotype -Patient study phenotype -phenotype -Cell culture study -Not clearly defined Phenotype-phenotype studies are annotated, if e.g. a mild form of a disease is compared to a severe form.

Patients/Control
If available, the number of healthy individuals (control) and disease affected patients is given. In such cases only the numbers are assigned. Disease affected animals are also assigned as patients.

Samples information
If the patients are differentiated in more detail, respective information is given in this text field.

Tissue/Cell line
The tissue or cell line analyzed in the publication is annotated using the terms from the tissue ontology (www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO).

Tissue/Cell line comment
Allows to include additional comments.

miRNA LIST


The miRNA list shows all differentially expressed miRNAs. The annotation relies on the miRBase 12.0 release. Outdated designations of miRNAs mentioned in publications are replaced by the currently valid names. Associated information is provided via the 'Detailed information about selected miRNA' field (see below). If a miRNA is ambiguously or not precisely described in the publication, only one variant of the miRNA is annotated. E.g. it was sometimes found that hsa-miR-320 is differentially regulated. Currently, in miRBase several variants of hsa-miR-320 exist. In such cases, only hsa-miR-320a is used for annotation of the miRNA-disease association. This issue is commented in the miRNA comment field (see "detailed information about selected miRNA). Foldchange (min-max): If the increase or decrease of miRNA is quantified, the available number is annotated in the '?fold change' fields.

Genes
The Genes field describes target genes of miRNAs. If available, additional information is provided in the linked information field 'Genes associated with selected miRNA' (see below).

Detailed information about selected miRNA
This section contains information about original miRNA designation from the authors of a study as well as information about the experimental methods used to quantify miRNA expression and the mode of regulation (up-/downregulation).

Genes associated with selected miRNA
Only experimentally verified target genes are annotated. Additionally, the way how the target gene expression is regulated by the miRNA (mRNA degradation, translational repression or both) is described. If target genes are cited, the PubMedID of the original paper is noted.