Organism : Methanococcus maripaludis S2 | Module List :
MMP0787

MarR family transcriptional regulator

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0787
(Mouseover regulator name to see its description)

Warning: No Regulators were found for MMP0787!

Warning: MMP0787 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
685 2.80e+02 cggcatTTTAtaAatCTAtaTgA
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686 1.60e+03 cgCTaGATtTTgATTGaTGCc
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895 1.60e+01 gtt.ggTg.TcAt.tgGcAaatc
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896 2.00e+02 CCAGGGTCTTTGAGC
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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 MMP0787

MMP0787 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for MMP0787

MMP0787 has total of 43 gene neighbors in modules 12, 121
Gene neighbors (43)
Gene Common Name Description Module membership
MMP0001 hypothetical protein MMP0001 46, 106, 121, 144
MMP0002 L-seryl-tRNA selenium transferase 12, 46, 76, 106, 121
MMP0007 geranylgeranylglyceryl phosphate synthase-like protein 12, 143
MMP0054 hypothetical protein MMP0054 76, 121
MMP0055 putative RNA-binding protein 76, 121
MMP0078 hypothetical protein MMP0078 12, 111
MMP0079 orotate phosphoribosyltransferase-like protein 12, 111
MMP0214 putative deoxyribonucleotide triphosphate pyrophosphatase 12, 104
MMP0289 hypD hydrogenase expression/formation protein HypD 12, 117
MMP0427 rfc replication factor C small subunit 12, 46
MMP0602 pyrF orotidine-5'-phosphate decarboxylase 12, 111
MMP0605 putative RNA-processing protein 12, 106
MMP0630 feoB ferrous iron transporter 28, 76, 106, 121
MMP0631 putative iron dependent repressor 28, 121, 144
MMP0684 hsp20 heat shock protein Hsp20 28, 121
MMP0686 fructose-bisphosphate aldolase 13, 121
MMP0787 MarR family transcriptional regulator 12, 121
MMP0808 hypothetical protein MMP0808 12, 106
MMP0809 phosphoribosylaminoimidazole carboxylase-like protein 12, 106
MMP0812 hypothetical protein MMP0812 12, 28
MMP0885 ATP/GTP-binding motif-containing protein 76, 121
MMP0902 hypothetical protein MMP0902 12, 49, 55
MMP1002 trpA tryptophan synthase subunit alpha 76, 121
MMP1003 trpB tryptophan synthase subunit beta 76, 121
MMP1004 trpF N-(5'-phosphoribosyl)anthranilate isomerase 76, 121
MMP1005 trpG anthranilate synthase component II 76, 121
MMP1006 trpE anthranilate synthase component I 76, 121
MMP1007 trpD anthranilate phosphoribosyltransferase 76, 121
MMP1008 trpC indole-3-glycerol-phosphate synthase 76, 121
MMP1026 argS arginyl-tRNA synthetase 12, 21
MMP1049 multiple resistance and pH regulation protein F 12, 99
MMP1051 surE stationary phase survival protein SurE 12, 28, 106
MMP1052 hypothetical protein MMP1052 12, 102
MMP1197 binding-protein dependent transport system inner membrane protein 12, 46
MMP1198 nitrate/sulfonate/bicarbonate ABC transporter ATPase 12, 143
MMP1217 hypothetical protein MMP1217 12, 46
MMP1218 hypothetical protein MMP1218 12, 46, 49
MMP1259 FAD-dependent pyridine nucleotide-disulfide oxidoreductase 12, 21
MMP1576 hypothetical protein MMP1576 12, 99
MMP1599 trkA TrkA-N domain-containing protein 76, 121
MMP1603 ferredoxin 12, 49
Unanno_36 None 46, 121
Unanno_55 None 76, 121
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 MMP0787
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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