Organism : Methanococcus maripaludis S2 | Module List :
MMP0559

hypothetical protein MMP0559

CircVis
Functional Annotations (2)
Function System
Putative intracellular protease/amidase cog/ cog
hydrolase activity, acting on glycosyl bonds go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0559
(Mouseover regulator name to see its description)

MMP0559 is regulated by 7 influences and regulates 0 modules.
Regulators for MMP0559 (7)
Regulator Module Operator
MMP0052
MMP0480
156 combiner
MMP0086 156 tf
MMP0168
MMP1100
156 combiner
MMP0217
MMP1023
156 combiner
MMP0217
MMP1646
156 combiner
MMP1023 156 tf
MMP1376 156 tf

Warning: MMP0559 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
807 3.50e+02 TaTCAcCcCc
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808 1.40e+03 cacGGaactatTGgA
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961 5.00e-06 ggGGGGA
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962 1.30e+03 cGGCGcTG
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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 MMP0559

MMP0559 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Putative intracellular protease/amidase cog/ cog
hydrolase activity, acting on glycosyl bonds go/ molecular_function
Module neighborhood information for MMP0559

MMP0559 has total of 34 gene neighbors in modules 73, 156
Gene neighbors (34)
Gene Common Name Description Module membership
MMP0128 cyclase family protein 73, 146, 153
MMP0182 hypothetical protein MMP0182 2, 73
MMP0215 hypothetical protein MMP0215 54, 156
MMP0283 ndk nucleoside diphosphate kinase 83, 156
MMP0292 hypothetical protein MMP0292 125, 156
MMP0293 aldolase 125, 156
MMP0311 hypothetical protein MMP0311 33, 73
MMP0312 hypothetical protein MMP0312 73, 94
MMP0313 hypothetical protein MMP0313 28, 73
MMP0335 hypothetical protein MMP0335 108, 156
MMP0456 xerD-like Phage integrase 73, 99
MMP0520 HAD superfamily ATPase 73, 146
MMP0542 hypothetical protein MMP0542 108, 156
MMP0559 hypothetical protein MMP0559 73, 156
MMP0628 TOBE domain-containing protein 108, 123, 156
MMP0678 hypothetical protein MMP0678 73, 76
MMP0691 hypothetical protein MMP0691 33, 73
MMP0709 hypothetical protein MMP0709 13, 156
MMP0848 peptide methionine sulfoxide reductase 73, 83
MMP0852 hypothetical protein MMP0852 125, 156
MMP0961 hypothetical protein MMP0961 74, 156
MMP0962 zinc finger protein 74, 156
MMP0963 MIP family channel protein 74, 156
MMP0976 hypothetical protein MMP0976 73, 83
MMP1160 hypothetical protein MMP1160 74, 84, 156
MMP1163 CutA1 divalent ion tolerance protein 74, 156
MMP1174 peroxiredoxin 125, 156
MMP1227 cbiE cobalt-precorrin-6Y C(5)-methyltransferase 73, 83
MMP1387 hypothetical protein MMP1387 33, 73, 150
MMP1683 hypothetical protein MMP1683 33, 73
MMP1720 hypothetical protein MMP1720 83, 156
MMP1721 hypothetical protein MMP1721 83, 156
Unanno_13 None 33, 73
Unanno_30 None 37, 73
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 MMP0559
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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