MyMpn
The Mycoplasma pneumoniae database
 
e.g Mpn001 or dnaN or polymerase
About ~ MyMpn Database
MyMpn: The database about Mycoplasma pneumoniae
 
DATA ACCESS:

  • Keyword/ID Search:
    • Search the gene/protein or the RNA table, respectively, using keywords or IDs, e.g. gene/protein: Mpn001 or dnaN or DNA polymerase III subunit beta or Cytoplasm or NP_109689 | rna: MPNs005.
  • BLAST Search:
    • Search the M. pneumoniae genome, the annotated genes, or RNAs either copying a base/an amino acid sequence into the provided box or uploading multifasta file. It is recommended to use amino acid sequences since base alignments with other organisms can be error-prone due to the specific codon usage, TGA codes for tryptophan not the end of a gene, of M. pneumoniae and its close relatives. The query type and the E-value cut-off have to be specified by the user.
  • Genomic Search
    • Specify a genomic region of interest and get the genes annotated in the specific region.
  • Browse Genes:
    • Visualize the complete table of annotated genes of M. pneumoniae.
  • Browse ncRNAs:
    • Visualize the complete table of annotated RNAs of M. pneumoniae.
  • Models:
    • Access the metabolic model iJW145 and a selection of simulation conditions and results.
  • Download/Analyze Data:
    • Normalized and preprocessed microarray data can be visualized (a link to the GEO data sets is provided, respectively) and the different '-omics' and 'comparative -omics' data sets with their corresponding resources are provided for download.

OMICS:

Genomics:

  • Genes
    • The Gene table contains the identifiers of the gene (Gene number, Gene name, Protein name, PID from the NCBI, Gene Id, GI and old MP number), and its characteristics (length, position , Strand, operon , nucleotide sequence of the ORF and of the 100 bps upstream of the initial methionine).
  • Gene essentiality
    • Essentiality is based on high through-put gene disruption studies. A gene is considered essential when no transposon insertion could be found for its ORF.
  • Operons
    • This table describes the operon organization of M. pneumoniae. Operons have been estimated combining data obtained from microarrays and tiling arrays experiments. Local convolution applied to tiling array data was used to elucidate reference operon boundaries. We further split the reference operons using tiling data of three time series. Split markers were put at positions where genes that showed different expression patterns (expressed vs non-expressed) with other members in the same reference operon. References were then split/ trimmed/ removed accordingly. In addition, operons are further subdivided based on the dissimilarity matrix. Monocistronic operons were not split. Bicistronic operons were split if genes showed a correlation below 0.6. Operons with 3 or more members are further subdivided by applying the algorithm PAM (Partitioning Around Medoids) to the dissimilarity matrix. Other information can be found in the table such as the presence of termination hairpins or the presence of -10 regions.

Transcriptomics:

  • Microarrays
    • The microarray experiments table shows the conditions under which the cells have been grown for the different experiments. "Experiment name" defines the type of experiment (Growth curve, Stringent response, Starvation, Adaptation), "condition" explains the type of experiment, "treatment" indicates the treatment applied to the cell compared to the "standard protocol". Finally, the experiment is described, the date of the experiment is shown, as well as the time of the experiment. The last column is the internal reference for the experimentalist. The microarray experiments were carried out following this protocol. Any changes in the growing conditions are described in the "Description" part of the table.

Proteomics:

  • Proteins
    • The protein table contains general information about M. pneumoniae proteins: identifiers (Gene number, Gene name, Protein number, Protein name, NCBI PID, UniProt entry, Swiss-Prot ID, RefSeq), its biochemical properties (Length, Molecular weight, Isoelectric point, Sequence), the structure prediction (PFAM domains, Interpro domains, Structures and PDB homologues), and some protein features (COG and Gene ontology, Localization, Pathway, EC number -if present).
  • Pfam domains
    • The Pfam domains table was obtained applying the Pfam algorithm to the M. pneumoniae sequences. Results are shown if the e-value is below 0.09. The table contains the gene number, the position and description of the domain, the e-value, the score, the Pfam accession number and the domain reference.
  • Complexes
    • These tables shows the prediction of new complexes in the M. pneumoniae proteome based on Tandem Affinity Purification-Mass Spectrometry data. It is divided into i) a set of 116 heteromultimeric complexes and ii) a set of 62 homomultimeric complexes. In part i) the first column on the left gives an assembly ID that specifies the higher order molecular assembly, which a heteromultimeric protein complex is clustering to. The second column specifies the unique complex ID for each protein complex. Columns 3 and 4 provide complex name and complex function, respectively. In columns 5-8 the gene number, gene name, UniProt protein name and subunit type of each protein component of a complex are delineated. In part ii) the first column on the left shows the complex ID of the homomultimeric protein complexes. The second column indicates the complex name. Columns 3 and 4 give the annotated gene number and gene name of each homomultimer. The fifth column highlights the multimerization state of each homomultimer, if known.
  • Peptides
    • This table shows the results of the mass spectrometry analysis of the M. pneumoniae proteome analysis. It indicates the amount of peptides generated for each gene, and the peptide coverage.

Metabolomics:

  • Metabolic reactions
    • Metabolic reconstruction is the result of the combination of genomic and experimental data, literature mining and sequence analysis. In this table, you will see for each reaction its KEGG references, the enzyme characteristics, the pathway and the equation of the reaction.
  • Growth curves
    • To confirm the different reactions and pathways from M. pneumoniae metabolism, medium composition was changed to include different substrates/metabolites (such as amino acids, bases, lipids, sugars, or vitamins). By clicking on the link, a plot of the growth curve will be displayed.

COMPARATIVE OMICS:

This section is dedicated to the comparison of M. pneumoniae and its closest relative M. genitalium.
  • Transcriptome
    • DSS Not Fractionated (6h and 96h) data files contain the direct strand specific sequencing of the M. pneumoniae transcriptome at exponential (6h) and stationary (96h) phases of growth. The table shows the pileup of RNAseq data for the different genome positions of plus and minus strand of the M. pneumoniae M129 reference.
    Small RNAs RNAseqStrandSpecific data files contain information about size-selected RNAs quantified by RNAseq at different times of growth.
    RNASeqStrandSpecificGrowth data files either show RNA copies per cell or the log2 of RPKM for genes and ncRNAs, both as results of RNAseq experiments.
  • Methylome
    • Mge 6 and 96h data files contain results of a genome methylation study in M. genitalium at exponential (6h) and stationary (96h) phases of growth facilitating information about genome position, strand, IPD ratios and p-values at 6 and 96 hours, respectively.
  • Genome
    • The files DataBase of Putative Peptides from Genome and Transcriptome, respectively, contain the peptide libraries obtained by in silico translating the theoretical coding capabilities of the genome and the experimentally determined transcriptome, respectively, applying a minimal threshold of 25aa. For each predicted ORF an internal ID, the genome position of the translational start codon (TSC), the strand, and the MPN ID - if existing - are displayed. Those libraries have been used for MS and sequencing analysis.
    The Genome Re-annotation data file contains the re-annotation of the M. pneumoniae genome based on transcriptomics and proteomics analyses. For each gene transcription start sites (TSSs), transcription termination sites (TTSs), genome position for the translational start codon (TSC), and the genome position of the stop codon (Stop) are shown.
    • Homology
      • Orthologs were obtained using the BLASTp program from NCBI against the Swiss-Prot library. Results are shown if the e-value is below 10-3. The table shows the query sequence, the UniProt accession number of the hit, the description of the hit, the e-value, the score, the position of the alignment in the hit, the length of the aligned hit sequence, the position alignment in the query sequence, the length of the aligned query sequence, and the overlap in percentage.
    • Orthology
  • Genome comparison of M. pneumoniae and M. genitalium
    • The genome comparison tool allows to explore similarities and differences between M. pneumoniae and M. genitalium.

3D ORGANIZATION:

Tomography pictures and a video showing the inside of an M. pneumoniae cell.


QUANTITATIVE BIOLOGY:

Statistical data of M. pneumoniae in comparison to other bacteria: Statistics about cellular properties, such as cell size, molecule numbers, energy costs for different cellular tasks, or average numbers for glycolytic intermediates for example, for M. pneumoniae and, if available for E. coli, B. subtilis, L. lactis, and several other bacteria.


GENOME BROWSERS:

  • MyGBrowse: This genome browser visualizes different genetic features, such as annotated genes and RNAs, transcription start and end sites, or hairpins, of M. pneumoniae for a genome cutout that can be specified by the user. The user can furthermore search for a specific gene of interest if (s)he does not know the exact location.
  • Gbrowser: This genome browser opens in a new window, thus providing a private session in which the user can upload personal tracks in order to compare his/her data with the content of the MyMpn database.

PATHWAY MAPS:

  • Metabolic map: A clickable metabolic map is provided that allows to zoom in on specific pathways, reactions, enzymes, and metabolites. Selecting a species (enzymes, metabolites) or a reaction by clicking on the respective flag will open a drop down menu with further information, including links MyMpn content and to external databases, on the selected entity.
  • Replication map: Molecular details of the DNA replication machinery.
  • DNA repair map: Molecular mechanisms of DNA repair processes.
Site hosted by:
Copyright 2010-16, Luis Serrano group. All rights reserved.
All data provided for download in the MyMpn database is free to use. Upon doing so, please cite the original data source and the MyMpn database
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