Organism : Halobacterium salinarum NRC-1 | Module List :
VNG1149Cm

metallo-beta-lactamase superfamily hydrolase

CircVis
Functional Annotations (2)
Function System
Predicted hydrolase of the metallo-beta-lactamase superfamily cog/ cog
hydrolase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG1149Cm
(Mouseover regulator name to see its description)

VNG1149Cm is regulated by 20 influences and regulates 0 modules.
Regulators for VNG1149Cm (20)
Regulator Module Operator
VNG0101G 23 tf
VNG1383G 23 tf
VNG2661G
VNG1029C
23 combiner
VNG6143H 23 tf
VNG0101G 33 tf
VNG1496G 33 tf
VNG6143H 33 tf
VNG0040C
VNG0293H
16 combiner
VNG0101G
VNG0320H
16 combiner
VNG0101G
VNG2163H
16 combiner
VNG1836G 16 tf
VNG2661G
VNG1029C
16 combiner
VNG0040C 2 tf
VNG0101G
VNG2163H
2 combiner
VNG0194H 2 tf
VNG0258H 2 tf
VNG1836G 2 tf
VNG2243G 2 tf
VNG2661G
VNG1029C
2 combiner
VNG2661G
VNG1123G
2 combiner

Warning: VNG1149Cm Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 8 motifs predicted.

Motif Table (8)
Motif Id e-value Consensus Motif Logo
983 6.60e+00 aAaaTcAAAacctaTaA.T
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984 1.10e+03 a.gaac.ccGcaAc.accttga.g
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1011 2.80e-04 caatttataggtTttcAcctt
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1012 1.20e+01 AaaagGGtTttcgTATcgccGT
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1023 1.00e+03 GaTtcaaAAgcaTaGa
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1024 2.90e+03 gTAAaA
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1043 1.70e+00 GaggacGc.gTCGAa
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1044 1.70e+03 cgtcgaC.AgctcGAcg.CgaGaa
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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 VNG1149Cm

VNG1149Cm is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted hydrolase of the metallo-beta-lactamase superfamily cog/ cog
hydrolase activity go/ molecular_function
Module neighborhood information for VNG1149Cm

VNG1149Cm has total of 89 gene neighbors in modules 2, 16, 23, 33
Gene neighbors (89)
Gene Common Name Description Module membership
VNG0013C hypothetical protein VNG0013C 2, 263
VNG0166G psmB proteasome subunit alpha 2, 275
VNG0192G ftsZ2 cell division protein FtsZ 2, 3, 7, 12, 16, 49, 50, 71, 78, 79, 123
VNG0194H hypothetical protein VNG0194H 3, 7, 12, 16, 50, 79, 123
VNG0207H hypothetical protein VNG0207H 2, 3, 7, 12, 16, 49, 67, 71, 78, 79, 113, 123
VNG0208H hypothetical protein VNG0208H 2, 3, 7, 12, 16, 24, 29, 49, 67, 71, 78, 79, 113, 123
VNG0209H hypothetical protein VNG0209H 2, 3, 7, 12, 16, 24, 29, 49, 67, 71, 78, 79, 113, 123
VNG0234C hypothetical protein VNG0234C 2, 16
VNG0258H hypothetical protein VNG0258H 3, 12, 16, 49, 79, 100, 109, 150
VNG0259G ipp inorganic pyrophosphatase 7, 12, 16, 79, 109
VNG0261H hypothetical protein VNG0261H 7, 12, 16, 25, 49, 50, 55, 79, 109, 113
VNG0524G yurY ABC transporter ATP-binding protein 2, 3, 7, 12, 16, 71, 113, 225
VNG0527C hypothetical protein VNG0527C 2, 3, 7, 12, 16, 71, 78, 79, 113, 123, 225
VNG0548C H/ACA RNA-protein complex component Nop10p 1, 10, 33, 39, 66, 82, 99, 137, 161, 180
VNG0549G eif2a translation initiation factor IF-2 subunit alpha 10, 33, 66, 82, 99, 137, 180
VNG0550G rps27e 30S ribosomal protein S27e 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180
VNG0551G rpl44e 50S ribosomal protein L44E 1, 10, 33, 39, 66, 82, 99, 137, 161, 180
VNG0582C hypothetical protein VNG0582C 16, 283
VNG0584H hypothetical protein VNG0584H 2, 16, 24
VNG0585H hypothetical protein VNG0585H 2, 16, 24
VNG0620G edp proteinase IV-like protein 2, 16
VNG0635G nolB NADH dehydrogenase/oxidoreductase-like protein 2, 16, 19, 24, 29, 199
VNG0637G ndhG5 NADH dehydrogenase/oxidoreductase 2, 16, 19, 24, 29
VNG0640G nolD NADH dehydrogenase/oxidoreductase-like protein 2, 3, 16, 19, 24, 29, 45, 123
VNG0642C hypothetical protein VNG0642C 2, 24, 29, 45
VNG0771G aldY2 AldY2 16, 123
VNG0789C hypothetical protein VNG0789C 10, 33, 99
VNG0790G rps15p 30S ribosomal protein S15P 10, 33, 99, 161
VNG0955G fapE flagella-like protein E 7, 16, 25, 50, 100, 291
VNG0960G flaB1 flagellin B1 2, 3, 7, 12, 16, 49, 78, 79, 100, 113, 123
VNG0961G flaB2 flagellin B2 2, 3, 7, 12, 16, 49, 78, 79, 100, 113, 123, 291
VNG0962G flaB3 flagellin B3 2, 3, 7, 12, 16, 49, 78, 100, 113, 123
VNG1132G rps13p 30S ribosomal protein S13P 1, 10, 33, 39, 66, 82, 137, 161, 165, 180
VNG1133G rps4p 30S ribosomal protein S4P 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180
VNG1134G rps11p 30S ribosomal protein S11P 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180
VNG1137G rpl18e 50S ribosomal protein L18e 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180
VNG1138G rpl13p 50S ribosomal protein L13P 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180
VNG1140G rpoN DNA-directed RNA polymerase subunit N 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180
VNG1141G rpoK DNA-directed RNA polymerase subunit K 1, 10, 33, 39, 66, 82, 99, 137, 161, 165, 180
VNG1149Cm metallo-beta-lactamase superfamily hydrolase 2, 16, 23, 33
VNG1150G idsA IdsA 33
VNG1158G rps28e 30S ribosomal protein S28e 23, 283
VNG1160G ndk nucleoside diphosphate kinase 23, 283
VNG1169C hypothetical protein VNG1169C 23, 66, 82, 137, 161, 165, 180
VNG1170G rpl21e 50S ribosomal protein L21e 23, 66, 82, 137, 161, 165
VNG1292H hypothetical protein VNG1292H 24, 33
VNG1294G slyD peptidyl-prolyl cis-trans isomerase 23, 67, 184
VNG1306G sdhA hypothetical protein VNG1306G 2, 3, 12, 16, 78, 79, 90, 100
VNG1308G sdhB hypothetical protein VNG1308G 2, 278
VNG1310G sdhC hypothetical protein VNG1310G 2, 24, 236
VNG1542G sucD hypothetical protein VNG1542G 33, 45, 67, 114, 124
VNG1689G rpl3p 50S ribosomal protein L3P 1, 10, 23, 39, 66, 82, 99, 137, 180
VNG1691G rplW 50S ribosomal protein L23P 1, 10, 23, 33, 39, 66, 82, 99, 137, 161, 165, 180
VNG1695G rpl22p 50S ribosomal protein L22P 1, 10, 23, 33, 39, 66, 82, 99, 137, 161, 165, 180
VNG1697G rps3p 30S ribosomal protein S3P 1, 10, 23, 33, 39, 66, 82, 99, 137, 165, 180
VNG1699C ribonuclease P protein component 1 1, 10, 23, 39, 99, 180, 227
VNG1701G rpl14p 50S ribosomal protein L14P 1, 10, 23, 137, 221
VNG1702G rpl24p 50S ribosomal protein L24P 1, 10, 23, 39, 66, 82, 99, 137, 165
VNG1705G rpl5p 50S ribosomal protein L5P 1, 10, 23, 39, 99, 180
VNG1706G rps14P 30S ribosomal protein S14P 10, 23, 221
VNG1709G rpl6p 50S ribosomal protein L6P 1, 10, 23, 39, 66, 99, 137, 165, 180
VNG1713G rpl19e 50S ribosomal protein L19e 1, 10, 23, 33, 39, 66, 99, 137, 180
VNG1718G rpl15p 50S ribosomal protein L15P 1, 10, 23, 39, 99, 180
VNG1719G secY preprotein translocase subunit SecY 1, 10, 23, 39, 99
VNG1768G eif5a translation initiation factor IF-5A 23, 24, 40, 59
VNG2053G rpoE' DNA-directed RNA polymerase subunit E' 33, 59
VNG2098H hypothetical protein VNG2098H 33
VNG2099C hypothetical protein VNG2099C 33, 45
VNG2135G atpD V-type ATP synthase subunit D 2, 16
VNG2139G atpA V-type ATP synthase subunit A 23, 24, 33, 39, 45, 67, 114, 124, 227
VNG2140G atpF V-type ATP synthase subunit F 33, 39, 45, 67, 114, 124, 227
VNG2141G atpC V-type ATP synthase subunit C 23, 39, 45, 67, 114, 124, 227
VNG2143G atpK H+-transporting ATP synthase subunit K 2, 19, 23, 24, 45, 67, 75, 114, 124, 227
VNG2144G atpI H+-transporting ATP synthase subunit I 19, 23, 24, 45, 67, 75, 124, 227
VNG2146H hypothetical protein VNG2146H 2, 16, 19, 24, 45, 67, 124, 227
VNG2151G etfA electron transfer flavoprotein subunit alpha 33, 45, 61, 124
VNG2337C hypothetical protein VNG2337C 16, 29, 49, 113
VNG2465C hypothetical protein VNG2465C 33, 184
VNG2467G rpl31e 50S ribosomal protein L31e 1, 33, 66, 82, 99, 137, 161, 165, 180
VNG2469G rpl39e 50S ribosomal protein L39e 1, 33, 66, 82, 99, 137, 161, 165, 180
VNG2574G can aconitate hydratase 23, 29
VNG2575G rimI Pab N-terminal acetyltransferase 23
VNG2648G rps10p 30S ribosomal protein S10P 2, 3, 16, 23, 24, 29, 40, 110
VNG2649G eef1a elongation factor 1-alpha 2, 3, 16, 24, 29, 40, 79, 110
VNG2654Gm EEF2 elongation factor EF-2 2, 23, 110
VNG2658G rps12P 30S ribosomal protein S12P 23, 39, 40, 45, 98, 110, 137
VNG2666G rpoB'' DNA-directed RNA polymerase subunit beta'' 2, 16, 40, 98, 110
VNG6294G perA peroxidase / catalase 23, 24, 29, 52
VNG6313G nhaC3 Na+/H+ antiporter 2, 3, 12, 16, 50, 113
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 VNG1149Cm
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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