Organism : Methanococcus maripaludis S2 | Module List :
MMP0070

tungsten containing formylmethanofruran dehydrogenase subunit C-like protein

CircVis
Functional Annotations (6)
Function System
Formylmethanofuran dehydrogenase subunit C cog/ cog
metabolic process go/ biological_process
formylmethanofuran dehydrogenase activity go/ molecular_function
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0070
(Mouseover regulator name to see its description)

MMP0070 is regulated by 13 influences and regulates 0 modules.
Regulators for MMP0070 (13)
Regulator Module Operator
H2 54 ef
MMP0499
MMP1065		 54 combiner
MMP0527 54 tf
MMP0907
MMP1646		 54 combiner
MMP1015 54 tf
H2 65 ef
MMP0052
MMP1304		 65 combiner
MMP0257
MMP1304		 65 combiner
MMP0499
MMP1015		 65 combiner
MMP1015 65 tf
MMP1065 65 tf
MMP1303 65 tf
MMP1304 65 tf

Warning: MMP0070 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
769 9.40e+00 gaAA.CtcCc
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770 5.80e+02 GGctTGcagA
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791 4.60e-03 cctcCtG.AgAg
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792 1.40e+02 CCCAaA.aAAAgAT
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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 MMP0070

MMP0070 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Formylmethanofuran dehydrogenase subunit C cog/ cog
metabolic process go/ biological_process
formylmethanofuran dehydrogenase activity go/ molecular_function
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for MMP0070

MMP0070 has total of 38 gene neighbors in modules 54, 65
Gene neighbors (38)
Gene Common Name Description Module membership
MMP0027 TrkA-N domain-containing protein 54, 57
MMP0070 tungsten containing formylmethanofruran dehydrogenase subunit C-like protein 54, 65
MMP0215 hypothetical protein MMP0215 54, 156
MMP0241 hypothetical protein MMP0241 65, 75
MMP0254 carbohydrate kinase 65, 101
MMP0276 hypothetical protein MMP0276 65, 94
MMP0455 amino-acid ABC transporter 54, 146
MMP0482 hypothetical protein MMP0482 54, 55
MMP0483 hypothetical protein MMP0483 54, 55
MMP0570 hypothetical protein MMP0570 22, 65
MMP0612 LigT 2'-5' RNA ligase 54, 57
MMP0621 xylose isomerase domain-containing protein 54, 57
MMP0638 hypothetical protein MMP0638 54, 55
MMP0642 hypothetical protein MMP0642 65, 145
MMP0643 hypothetical protein MMP0643 49, 65
MMP0672 binding-protein dependent transport system inner membrane protein 37, 54
MMP0693 aminoacyl-tRNA synthetase, class II 33, 54
MMP0753 hypothetical protein MMP0753 65, 154
MMP0764 hypothetical protein MMP0764 30, 65
MMP0765 hypothetical protein MMP0765 30, 65
MMP0770 ABC transporter 30, 65
MMP0863 CBS domain-containing protein 2, 54, 146
MMP0903 hypothetical protein MMP0903 33, 54, 55
MMP0915 cobY/cofC nucleoside triphosphate: 5'-deoxyadenosylcobinamide phosphate nucleotidyltransferase 30, 65
MMP0916 PRC-barrel domain-containing protein 30, 65
MMP0991 hypothetical protein MMP0991 22, 65
MMP1029 hypothetical protein MMP1029 65, 152
MMP1053 hdrB2 heterodisulfide reductase subunit B2 9, 65
MMP1054 hdrC2 heterodisulfide reductase subunit C2 9, 65
MMP1234 UBA/THIF-type NAD/FAD binding protein 33, 54, 55, 106
MMP1552 3-octaprenyl-4-hydroxybenzoate carboxy-lyase 54, 150
MMP1605 pyruvate kinase 1, 54, 146, 166
MMP1636 major facilitator transporter 22, 65, 153
MMP1641 soluble P-type ATPase 54, 57
MMP1684 metallophosphoesterase 65, 101
Unanno_32 None 65, 123
Unanno_34 None 65, 101
Unanno_44 None 65, 154
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 MMP0070
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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