Organism : Methanococcus maripaludis S2 | Module List :
MMP0912

4-oxalocrotonate tautomerase

CircVis
Functional Annotations (6)
Function System
Uncharacterized protein, 4-oxalocrotonate tautomerase homolog cog/ cog
cellular aromatic compound metabolic process go/ biological_process
isomerase activity go/ molecular_function
Benzoate degradation 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 MMP0912
(Mouseover regulator name to see its description)

MMP0912 is regulated by 11 influences and regulates 0 modules.
Regulators for MMP0912 (11)
Regulator Module Operator
H2 74 ef
MMP0052
MMP0480
74 combiner
MMP0086 74 tf
MMP0097
MMP1376
74 combiner
MMP0217
MMP1023
74 combiner
MMP0217
MMP1646
74 combiner
MMP1376 74 tf
MMP0052
MMP0480
50 combiner
MMP0086 50 tf
MMP0217
MMP1646
50 combiner
MMP0460 50 tf

Warning: MMP0912 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
761 6.50e+01 TT.ggGgGAT
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762 1.30e+02 CCT.TTtcgcC
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809 9.00e+00 C.gCcCgc
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810 1.80e+02 GGGGGA
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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 MMP0912

MMP0912 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Uncharacterized protein, 4-oxalocrotonate tautomerase homolog cog/ cog
cellular aromatic compound metabolic process go/ biological_process
isomerase activity go/ molecular_function
Benzoate degradation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for MMP0912

MMP0912 has total of 33 gene neighbors in modules 50, 74
Gene neighbors (33)
Gene Common Name Description Module membership
Antisense_27 None 19, 50
MMP0123 purT phosphoribosylglycinamide formyltransferase 2 50, 123
MMP0184 riboflavin kinase 45, 50
MMP0373 hypothetical protein MMP0373 46, 50
MMP0387 microsomal signal peptidase 21 KD subunit 46, 50
MMP0558 hypothetical protein MMP0558 50, 166
MMP0622 ADP-ribosylation/crystallin J1 50, 90
MMP0624 hypothetical protein MMP0624 50, 123
MMP0633 rubrerythrin 13, 50
MMP0683 ftsY signal recognition particle-docking protein FtsY 50, 123
MMP0692 hypothetical protein MMP0692 50, 83
MMP0864 napA-2 Na+/H+ exchanger 50, 146, 166
MMP0912 4-oxalocrotonate tautomerase 50, 74
MMP0913 hypothetical protein MMP0913 50, 74, 84
MMP0914 hypothetical protein MMP0914 50, 74, 84
MMP0961 hypothetical protein MMP0961 74, 156
MMP0962 zinc finger protein 74, 156
MMP0963 MIP family channel protein 74, 156
MMP1154 hdrC1 heterosulfide reductase subunit C1 74, 84, 123
MMP1155 hdrB1 heterosulfide reductase subunit B1 74, 84
MMP1156 carboxymuconolactone decarboxylase 74, 84, 108, 123
MMP1157 rbo desulfoferrodoxin, ferrous iron-binding site 74, 84
MMP1158 hypothetical protein MMP1158 74, 84, 123
MMP1159 Ferritin 74, 84
MMP1160 hypothetical protein MMP1160 74, 84, 156
MMP1161 hypothetical protein MMP1161 74, 84
MMP1163 CutA1 divalent ion tolerance protein 74, 156
MMP1220 glgP alpha-glucan phosphorylase 50, 75
MMP1237 hypothetical protein MMP1237 50, 150
MMP1475 hypothetical protein MMP1475 19, 50
MMP1613 ssh10b_1 DNA/RNA-binding protein albA 13, 50
MMP1635 redox-active disulfide protein 1 13, 50
MMP1654 hypothetical protein MMP1654 50, 166
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 MMP0912
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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