Organism : Halobacterium salinarum NRC-1 | Module List :
VNG0790G rps15p

30S ribosomal protein S15P

CircVis
Functional Annotations (5)
Function System
Ribosomal protein S15P/S13E cog/ cog
structural constituent of ribosome go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
Ribosome kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG0790G
(Mouseover regulator name to see its description)

VNG0790G is regulated by 13 influences and regulates 0 modules.
Regulators for VNG0790G rps15p (13)
Regulator Module Operator
VNG0101G 161 tf
VNG0315G 161 tf
VNG0374G
VNG0315G
161 combiner
VNG2661G
VNG1483C
161 combiner
VNG0101G 33 tf
VNG1496G 33 tf
VNG6143H 33 tf
VNG0101G 10 tf
VNG0315G 10 tf
VNG0374G
VNG0315G
10 combiner
VNG2661G 10 tf
VNG0101G 99 tf
VNG2661G 99 tf

Warning: VNG0790G 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
999 2.50e+02 gc.cGa.A.cctcCGCCTggtt.A
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1000 2.70e+03 GAGtCCGAGaA
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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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1173 3.70e+00 gt.cGa.atcctcCGCCTggttaA
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1174 1.50e+03 aC.AgCtcGagccccAGAAca
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1283 6.30e+02 GtGTcGAAtCG
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1284 1.20e+04 GA.A.G.TtCGcCTGtTtaA
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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 VNG0790G

VNG0790G is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Ribosomal protein S15P/S13E cog/ cog
structural constituent of ribosome go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
Ribosome kegg/ kegg pathway
Module neighborhood information for VNG0790G

VNG0790G has total of 66 gene neighbors in modules 10, 33, 99, 161
Gene neighbors (66)
Gene Common Name Description Module membership
VNG0177G rpl15e 50S ribosomal protein L15e 161, 266
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
VNG0789C hypothetical protein VNG0789C 10, 33, 99
VNG0790G rps15p 30S ribosomal protein S15P 10, 33, 99, 161
VNG1103G rpl12p 50S ribosomal protein L12P 1, 10, 39, 66, 82, 99, 137, 150, 161, 165, 180
VNG1104G rplP0 acidic ribosomal protein P0 1, 10, 39, 66, 82, 99, 137, 150, 161, 165, 180
VNG1105G rpl1P 50S ribosomal protein L1P 1, 10, 39, 66, 82, 99, 137, 150, 161, 165, 180
VNG1108G rpl11p 50S ribosomal protein L11P 1, 66, 82, 137, 150, 161, 165, 180
VNG1111G drg GTP-binding protein DRG 1, 82, 137, 150, 161
VNG1114G glo1 glyoxalase 1, 82, 137, 150, 161, 165, 180
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
VNG1136G rpb3 DNA-directed RNA polymerase II 1, 10, 39, 66, 82, 137, 161, 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
VNG1139Gm rps9p 30S ribosomal protein S9P 1, 10, 39, 161
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
VNG1142G eno phosphopyruvate hydratase 1, 10, 39, 161
VNG1143G rps2P 30S ribosomal protein S2 1, 10
VNG1149Cm metallo-beta-lactamase superfamily hydrolase 2, 16, 23, 33
VNG1150G idsA IdsA 33
VNG1169C hypothetical protein VNG1169C 23, 66, 82, 137, 161, 165, 180
VNG1170G rpl21e 50S ribosomal protein L21e 23, 66, 82, 137, 161, 165
VNG1289H hypothetical protein VNG1289H 161
VNG1292H hypothetical protein VNG1292H 24, 33
VNG1494G rpl37e 50S ribosomal protein L37e 161, 165
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
VNG1690G rpl4lp 50S ribosomal protein L4P 1, 10, 39, 66, 82, 99, 137, 161, 165, 180
VNG1691G rplW 50S ribosomal protein L23P 1, 10, 23, 33, 39, 66, 82, 99, 137, 161, 165, 180
VNG1692G rpl2p 50S ribosomal protein L2P 1, 10, 66, 99, 165
VNG1693G rps19p 30S ribosomal protein S19P 1, 10, 66, 99, 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
VNG1698G rpmC 50S ribosomal protein L29P 10
VNG1699C ribonuclease P protein component 1 1, 10, 23, 39, 99, 180, 227
VNG1700G rps17p 30S ribosomal protein S17P 1, 10
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
VNG1703G rps4e 30S ribosomal protein S4e 10, 221
VNG1705G rpl5p 50S ribosomal protein L5P 1, 10, 23, 39, 99, 180
VNG1706G rps14P 30S ribosomal protein S14P 10, 23, 221
VNG1707G rps8p 30S ribosomal protein S8P 1, 10, 66, 99
VNG1709G rpl6p 50S ribosomal protein L6P 1, 10, 23, 39, 66, 99, 137, 165, 180
VNG1711G rpl32e 50S ribosomal protein L32e 10
VNG1713G rpl19e 50S ribosomal protein L19e 1, 10, 23, 33, 39, 66, 99, 137, 180
VNG1714G rpl18p 50S ribosomal protein L18P 10, 39, 99
VNG1715G rps5p 30S ribosomal protein S5P 10
VNG1716G rpl30p 50S ribosomal protein L30P 10, 99, 221
VNG1718G rpl15p 50S ribosomal protein L15P 1, 10, 23, 39, 99, 180
VNG1719G secY preprotein translocase subunit SecY 1, 10, 23, 39, 99
VNG2053G rpoE' DNA-directed RNA polymerase subunit E' 33, 59
VNG2098H hypothetical protein VNG2098H 33
VNG2099C hypothetical protein VNG2099C 33, 45
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
VNG2151G etfA electron transfer flavoprotein subunit alpha 33, 45, 61, 124
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
VNG2514G rps6e 30S ribosomal protein S6e 1, 10
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 VNG0790G
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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