Organism : Methanococcus maripaludis S2 | Module List :
MMP1058

hypothetical protein MMP1058

CircVis
Functional Annotations (1)
Function System
Uncharacterized conserved protein cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1058
(Mouseover regulator name to see its description)

MMP1058 is regulated by 7 influences and regulates 0 modules.
Regulators for MMP1058 (7)
Regulator Module Operator
MMP1065 13 tf
MMP1447 13 tf
MMP0052
MMP0480		 83 combiner
MMP0460 83 tf
MMP0907
MMP1646		 83 combiner
MMP1023
MMP1303		 83 combiner
MMP1065 83 tf

Warning: MMP1058 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
687 9.70e+00 tCgcgGg.aCT
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688 1.90e+04 GGatCTtGGGG
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827 6.90e+00 TtCaCCccg
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828 1.90e+02 CCtgCAcc
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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 MMP1058

MMP1058 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Uncharacterized conserved protein cog/ cog
Module neighborhood information for MMP1058

MMP1058 has total of 45 gene neighbors in modules 13, 83
Gene neighbors (45)
Gene Common Name Description Module membership
MMP0022 hypothetical protein MMP0022 13, 66
MMP0023 hypothetical protein MMP0023 13, 66
MMP0052 putative CBS domain-containing signal transduction protein 13, 117
MMP0129 hypothetical protein MMP0129 37, 83
MMP0154 hypothetical protein MMP0154 1, 13
MMP0177 hypothetical protein MMP0177 83, 117, 152
MMP0226 ExsB family transcriptional regulator 13, 117
MMP0283 ndk nucleoside diphosphate kinase 83, 156
MMP0336 hjc Holliday junction resolvase 13, 94
MMP0337 hypothetical protein MMP0337 13, 94
MMP0420 CBS domain-containing protein 13, 106
MMP0421 hypothetical protein MMP0421 13, 83
MMP0422 hypothetical protein MMP0422 13, 83
MMP0449 ferredoxin 13, 70
MMP0585 UspA domain-containing protein 83, 151, 152
MMP0633 rubrerythrin 13, 50
MMP0660 apt adenine phosphoribosyltransferase 83, 94, 152
MMP0686 fructose-bisphosphate aldolase 13, 121
MMP0687 tpiA triosephosphate isomerase 8, 13
MMP0692 hypothetical protein MMP0692 50, 83
MMP0709 hypothetical protein MMP0709 13, 156
MMP0848 peptide methionine sulfoxide reductase 73, 83
MMP0940 hypothetical protein MMP0940 83, 119
MMP0976 hypothetical protein MMP0976 73, 83
MMP1016 putative CBS domain-containing signal transduction protein 13, 123
MMP1058 hypothetical protein MMP1058 13, 83
MMP1118 hypothetical protein MMP1118 83, 117
MMP1221 SAM-binding motif-containing protein 46, 83
MMP1227 cbiE cobalt-precorrin-6Y C(5)-methyltransferase 73, 83
MMP1250 6-pyruvoyl tetrahydropterin synthase 83, 145
MMP1358 ferredoxin 13, 21
MMP1397 smc1 structural maintenance of chromosome protein 13, 83
MMP1428 hypothetical protein MMP1428 55, 83
MMP1533 hypothetical protein MMP1533 13, 123
MMP1534 hypothetical protein MMP1534 13, 123
MMP1551 ffh signal recognition particle protein Srp54 49, 55, 83
MMP1568 hypothetical protein MMP1568 83, 119
MMP1569 hypothetical protein MMP1569 83, 119
MMP1606 flavoprotein:DNA/pantothenate metabolism flavoprotein 1, 13, 49
MMP1607 hypothetical protein MMP1607 49, 55, 83
MMP1613 ssh10b_1 DNA/RNA-binding protein albA 13, 50
MMP1635 redox-active disulfide protein 1 13, 50
MMP1637 hypothetical protein MMP1637 13, 19
MMP1720 hypothetical protein MMP1720 83, 156
MMP1721 hypothetical protein MMP1721 83, 156
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 MMP1058
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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