Organism : Methanococcus maripaludis S2 | Module List :
MMP0259 rplP0

acidic ribosomal protein P0

CircVis
Functional Annotations (5)
Function System
Ribosomal protein L10 cog/ cog
intracellular go/ cellular_component
translational elongation go/ biological_process
ribosome biogenesis go/ biological_process
Ribosome kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0259
(Mouseover regulator name to see its description)

MMP0259 is regulated by 20 influences and regulates 0 modules.
Regulators for MMP0259 rplP0 (20)
Regulator Module Operator
MMP0209 56 tf
MMP0257
MMP1447
56 combiner
MMP0460 56 tf
MMP0568 56 tf
MMP0700
MMP1347
56 combiner
MMP1347 56 tf
MMP0041 11 tf
MMP0052 11 tf
MMP0097 11 tf
MMP0097
MMP0631
11 combiner
MMP0568 11 tf
MMP0032
MMP0097
18 combiner
MMP0033 18 tf
MMP0052 18 tf
MMP0052
MMP0097
18 combiner
MMP0052
MMP0257
18 combiner
MMP0097
MMP0674
18 combiner
MMP0097
MMP0752
18 combiner
MMP0097
MMP1052
18 combiner
MMP0568 18 tf

Warning: MMP0259 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
683 1.90e+02 ctCaCC
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684 3.70e+02 gtCCCA
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697 1.80e+01 ATgg.Aaa.gCcCtA
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698 1.90e+02 gCCCCA
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773 1.50e+01 GGcGCg
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774 1.30e+02 GGAGGt
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for MMP0259

MMP0259 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Ribosomal protein L10 cog/ cog
intracellular go/ cellular_component
translational elongation go/ biological_process
ribosome biogenesis go/ biological_process
Ribosome kegg/ kegg pathway
Module neighborhood information for MMP0259

MMP0259 has total of 33 gene neighbors in modules 11, 18, 56
Gene neighbors (33)
Gene Common Name Description Module membership
MMP0044 beta-lactamase domain-containing protein 11, 20
MMP0093 50S ribosomal protein L21e 8, 11, 20
MMP0094 putative pseudouridylate synthase 8, 11
MMP0150 hypothetical protein MMP0150 11, 138
MMP0151 rpl40e 50S ribosomal protein L40e 11, 138
MMP0158 hypothetical protein MMP0158 18, 91
MMP0159 rpl39e 50S ribosomal protein L39e 11, 18, 105
MMP0258 rpl12p 50S ribosomal protein L12P 11, 103
MMP0259 rplP0 acidic ribosomal protein P0 11, 18, 56
MMP0260 rpl1P 50S ribosomal protein L1P 18, 56
MMP0298 rpl15 50S ribosomal protein L15e 18, 128
MMP0572 slyD FKBP-type peptidylprolyl isomerase 11, 96
MMP0574 hypothetical protein MMP0574 11, 138
MMP0575 gatC aspartyl/glutamyl-tRNA amidotransferase subunit C 11, 138
MMP0576 dapA dihydrodipicolinate synthase 11, 18, 138
MMP0577 rps17E 30S ribosomal protein S17e 11, 18, 138
MMP0578 aroQ chorismate mutase 11, 18, 96, 138
MMP0625 50S ribosomal protein L14e 11, 18, 105
MMP0626 cmk cytidylate kinase 18, 56
MMP0627 rpl34e 50S ribosomal protein L34e 18, 56, 79
MMP0971 purB adenylosuccinate lyase 8, 11
MMP1147 rpl37e 50S ribosomal protein L37e 18, 96, 138
MMP1472 hypothetical protein MMP1472 11, 61
MMP1473 hypothetical protein MMP1473 11, 20
MMP1509 hypothetical protein MMP1509 11, 20
MMP1544 rpl4lp 50S ribosomal protein L4P 56, 63, 128
MMP1545 rplW 50S ribosomal protein L23P 56, 63, 128
MMP1546 rpl2p 50S ribosomal protein L2P 56, 128
MMP1547 rps19p 30S ribosomal protein S19P 56, 128
MMP1584 spermidine synthase 11, 21
MMP1705 creatininase 8, 11, 20
MMP1708 rps27e 30S ribosomal protein S27e 11, 20
MMP1709 rpl44e 50S ribosomal protein L44e 11, 20
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for MMP0259
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend