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associated data and services are for academic, non-commercial use only.
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information which have been provided through this server. Neither the use
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products to any third parties is permitted.
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.
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.
PubMed ID of the annotated article.
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
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.
The field provides information about the
general design of the study. The following terms are available:
-Patient study control
-Patient study 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.
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.
If the patients are differentiated in more
detail, respective information is given in this text field.
The tissue or cell line analyzed in the
publication is annotated using the terms from the tissue ontology
Tissue/Cell line comment
Allows to include additional comments.
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
The Genes field describes target genes of
miRNAs. If available, additional information is provided in the
linked information field 'Genes associated with selected miRNA'
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.