Organism : Methanococcus maripaludis S2 | Module List :
MMP0092 rpoF

DNA-directed RNA polymerase subunit F

CircVis
Functional Annotations (11)
Function System
Uncharacterized protein conserved in archaea cog/ cog
nucleotide binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0092
(Mouseover regulator name to see its description)

MMP0092 is regulated by 5 influences and regulates 0 modules.
Regulators for MMP0092 rpoF (5)
Regulator Module Operator
MMP0052
MMP0257		 87 combiner
MMP0607
MMP1442		 87 combiner
MMP1023
MMP1303		 87 combiner
MMP0052
MMP0257		 109 combiner
MMP0907
MMP1646		 109 combiner

Warning: MMP0092 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
833 3.60e+02 cCaacaATccGgC
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834 3.80e+03 CaccTGcTGAG
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875 2.20e+02 GGaGgc
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876 8.70e+03 GCGAGAaG
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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 MMP0092

MMP0092 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Uncharacterized protein conserved in archaea cog/ cog
nucleotide binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
Module neighborhood information for MMP0092

MMP0092 has total of 29 gene neighbors in modules 87, 109
Gene neighbors (29)
Gene Common Name Description Module membership
Antisense_4 None 80, 87
MMP0033 LysR family protein 87, 109
MMP0036 tfe transcription initiation factor E subunit alpha 49, 87, 92, 129
MMP0092 rpoF DNA-directed RNA polymerase subunit F 87, 109
MMP0155 hypothetical protein MMP0155 61, 87
MMP0246 hypothetical protein MMP0246 87, 109
MMP0247 ribosomal biogenesis protein 87, 109
MMP0248 DNA-directed RNA polymerase-like protein 87, 109
MMP0316 iorA1 indolepyruvate oxidoreductase subunit alpha 1 25, 64, 87
MMP0384 hypothetical protein MMP0384 61, 87
MMP0398 hypothetical protein MMP0398 70, 80, 87
MMP0403 hypothetical protein MMP0403 87, 115
MMP0404 cofD 2-phospho-L-lactate transferase 87, 137
MMP0412 MiaB-like tRNA modifying protein 4, 25, 87
MMP0566 AMP-binding domain-containing protein 92, 109
MMP0568 transcriptional regulator-like protein 109, 162
MMP0603 aIF-1A translation initiation factor IF-1A 29, 87, 109, 162
MMP0604 hypothetical protein MMP0604 87, 109
MMP0671 ywbE hypothetical protein MMP0671 51, 87
MMP0694 beta-lactamase-like protein 51, 109, 149
MMP0707 sodium/hydrogen exchanger 87, 109, 140
MMP0878 ribonuclease P-like protein 25, 87, 140
MMP1114 rpe Pentose-5-phosphate 3-epimerase 109, 120
MMP1115 transketolase, N terminal half 109, 120
MMP1361 rpoB2 DNA-directed RNA polymerase subunit beta'' 25, 92, 109, 149
MMP1425 tRNA 2'-O-methylase 25, 87, 140
MMP1480 aconitase family 60, 87, 92
MMP1582 pdaD pyruvoyl-dependent arginine decarboxylase 87, 149
MMP1710 hypothetical protein MMP1710 20, 87, 92
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 MMP0092
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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