Organism : Methanococcus maripaludis S2 | Module List :
MMP0009

putative DNA primase large subunit

CircVis
Functional Annotations (8)
Function System
Eukaryotic-type DNA primase, large subunit cog/ cog
DNA primase activity go/ molecular_function
alpha DNA polymerase:primase complex go/ cellular_component
DNA replication, synthesis of RNA primer go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
DNA replication kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0009
(Mouseover regulator name to see its description)

MMP0009 is regulated by 7 influences and regulates 0 modules.
Regulators for MMP0009 (7)
Regulator Module Operator
MMP0018
MMP0402
75 combiner
MMP0097
MMP0631
75 combiner
MMP0209 75 tf
MMP0402
MMP1015
75 combiner
MMP1023 75 tf
MMP0499
MMP1015
151 combiner
MMP0499
MMP1065
151 combiner

Warning: MMP0009 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
811 9.70e-01 CCcctCcg
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812 7.10e+03 aAAAtA.ccGA
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951 1.70e-02 CGggGGgA
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952 9.70e+02 ggcgGcTggA
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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 MMP0009

MMP0009 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Eukaryotic-type DNA primase, large subunit cog/ cog
DNA primase activity go/ molecular_function
alpha DNA polymerase:primase complex go/ cellular_component
DNA replication, synthesis of RNA primer go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
DNA replication kegg/ kegg pathway
Module neighborhood information for MMP0009

MMP0009 has total of 48 gene neighbors in modules 75, 151
Gene neighbors (48)
Gene Common Name Description Module membership
Antisense_21 None 37, 119, 151
MMP0008 DP1 DNA polymerase II small subunit 22, 75, 142
MMP0009 putative DNA primase large subunit 75, 151
MMP0063 argB acetylglutamate kinase 49, 151
MMP0090 glycosyl transferase 69, 110, 151
MMP0113 hypothetical protein MMP0113 23, 75, 142
MMP0119 birA biotin--acetyl-CoA-carboxylase ligase 1, 75, 142
MMP0235 hypothetical protein MMP0235 75, 160
MMP0236 hypothetical protein MMP0236 75, 104
MMP0237 hypothetical protein MMP0237 75, 160
MMP0239 hypothetical protein MMP0239 1, 49, 75, 106
MMP0240 hypothetical protein MMP0240 75, 160
MMP0241 hypothetical protein MMP0241 65, 75
MMP0369 hypothetical protein MMP0369 58, 151
MMP0392 purD phosphoribosylamine--glycine ligase 4, 75, 104
MMP0452 hypothetical protein MMP0452 75, 160
MMP0453 neutral zinc metallopeptidase 22, 75
MMP0458 hypothetical protein MMP0458 75, 160
MMP0475 hypothetical protein MMP0475 26, 31, 45, 72, 82, 151
MMP0515 modB molybdenum ABC transporter permease 6, 53, 72, 110, 151
MMP0585 UspA domain-containing protein 83, 151, 152
MMP0595 hypothetical protein MMP0595 75, 160
MMP0598 phosphoglycerate mutase-related 106, 151
MMP0614 iron-sulfur flavoprotein 43, 125, 151
MMP0635 ABC transporter ATPase 75, 108
MMP0636 hypothetical protein MMP0636 75, 160
MMP0723 hypothetical protein MMP0723 75, 160
MMP0725 putative integral membrane protein 49, 75, 90, 151
MMP0769 hypothetical protein MMP0769 36, 53, 151, 161
MMP0886 cobalt ABC transporter inner membrane protein 4, 151
MMP0909 hypothetical protein MMP0909 75, 104
MMP0934 hypothetical protein MMP0934 75, 126
MMP0939 HAD superfamily (subfamily IA) hydrolase 46, 151
MMP1056 hypothetical protein MMP1056 119, 151
MMP1141 ATP-dependent helicase 75, 142
MMP1162 beta-lactamase domain-containing protein 75, 108
MMP1179 methyltransferase 85, 110, 151
MMP1220 glgP alpha-glucan phosphorylase 50, 75
MMP1262 hypothetical protein MMP1262 14, 151
MMP1295 glucose-6-phosphate isomerase 43, 75
MMP1343 hypothetical protein MMP1343 49, 151
MMP1388 redox-active disulfide protein 2 99, 151
MMP1525 modulator of DNA gyrase 100, 151
MMP1526 rncS ribonuclease III family protein 36, 53, 151
MMP1679 hypothetical protein MMP1679 117, 151
RNA_23 tRNA-Glu2 Glu tRNA 88, 100, 101, 151, 165
RNA_47 rrnB5S 5S ribosomal RNA 100, 101, 151
Unanno_43 None 62, 151
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 MMP0009
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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