Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2722 cysS

Cysteinyl-tRNA synthetase, class Ia (NCBI)

CircVis
Functional Annotations (7)
Function System
Cysteinyl-tRNA synthetase cog/ cog
cysteine-tRNA ligase activity go/ molecular_function
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
cysteinyl-tRNA aminoacylation go/ biological_process
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
cysS tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2722
(Mouseover regulator name to see its description)

RSP_2722 is regulated by 14 influences and regulates 0 modules.
Regulators for RSP_2722 cysS (14)
Regulator Module Operator
RSP_1231 30 tf
RSP_2346 30 tf
RSP_0386 214 tf
RSP_0443 214 tf
RSP_0623 214 tf
RSP_0760 214 tf
RSP_1518 214 tf
RSP_2324 214 tf
RSP_2346 214 tf
RSP_2494 214 tf
RSP_2572 214 tf
RSP_2963 214 tf
RSP_3616 214 tf
RSP_3665 214 tf

Warning: RSP_2722 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
7780 7.00e-02 ct.TtCtCctcaTc.c
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7781 1.10e+03 CccgcaAAgggcAAgAgcaTtc
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8148 6.50e-12 cgAAc.tttCtTtcgcaacaaa.
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8149 8.40e-03 AAgTcacttga
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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 RSP_2722

RSP_2722 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Cysteinyl-tRNA synthetase cog/ cog
cysteine-tRNA ligase activity go/ molecular_function
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
cysteinyl-tRNA aminoacylation go/ biological_process
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
cysS tigr/ tigrfam
Module neighborhood information for RSP_2722

RSP_2722 has total of 45 gene neighbors in modules 30, 214
Gene neighbors (45)
Gene Common Name Description Module membership
RSP_0150 RSP_0150 chase sensor signal transducdtion histidine kinase (NCBI) 87, 214
RSP_0353 RSP_0353 None 30, 297
RSP_0452 recA Recombinase A, DNA recombination protein (NCBI) 30, 93
RSP_0613 RSP_0613 hypothetical protein (NCBI) 214, 325
RSP_0657 RSP_0657 hypothetical protein (NCBI) 30, 72
RSP_0658 RSP_0658 Probable ATP-dependent helicase (NCBI) 30, 72
RSP_0659 RSP_0659 Putative metallo-phosphoesterase (NCBI) 30, 72
RSP_0760 mucS transcriptional regulator, MarR family (NCBI) 17, 214
RSP_0863 leuC 3-isopropylmalate dehydratase large subunit (NCBI) 30, 203
RSP_1041 RSP_1041 Malonyl CoA synthetase (NCBI) 214, 363
RSP_1127 ElaA acetyltransferase, GNAT family (NCBI) 214, 231
RSP_1360 RSP_1360 hypothetical protein (NCBI) 30, 93
RSP_1410 RSP_1410 hypothetical protein (NCBI) 2, 30
RSP_1489 RSP_1489 Protein containing thioredoxin domain (NCBI) 30, 71
RSP_1606 RSP_1606 Putative regulatory protein, GntR family (NCBI) 32, 214
RSP_1607 RSP_1607 Putative regulatory protein, GntR family (NCBI) 77, 214
RSP_1608 RSP_1608 Putative Zn-dependent dehydrogenase (NCBI) 32, 214
RSP_1609 RSP_1609 Putative altronate dehydrogenase (NCBI) 32, 214
RSP_1610 RSP_1610 altronate hydrolase (NCBI) 32, 214
RSP_1893 RSP_1893 Inositol monophosphatase family protein (NCBI) 214, 240
RSP_1926 RSP_1926 tRNA-Dihydrouridine synthase (NCBI) 214, 311
RSP_1997 lexA LexA repressor (NCBI) 30, 93
RSP_1998 RSP_1998 Molybdenum cofactor biosynthesis protein A (NCBI) 30, 114
RSP_2000 RSP_2000 molybdenum cofactor biosynthesis protein C (NCBI) 30, 207
RSP_2188 RSP_2188 hypothetical protein (NCBI) 175, 214
RSP_2189 pccB propionyl-CoA carboxylase beta chain (NCBI) 121, 214
RSP_2230 RSP_2230 response regulator receiver domain protein (NCBI) 214, 353
RSP_2457 RSP_2457 hypothetical protein (NCBI) 30, 267
RSP_2460 alr alanine racemase (NCBI) 30, 369
RSP_2624 RSP_2624 hypothetical protein (NCBI) 30, 93
RSP_2696 RSP_2696 ABC transporter, fused ATPase and inner membrane subunits (NCBI) 214, 311
RSP_2717 RSP_2717 putative UUP ATPase (NCBI) 214, 311
RSP_2722 cysS Cysteinyl-tRNA synthetase, class Ia (NCBI) 30, 214
RSP_2744 RSP_2744 hypothetical protein (NCBI) 214, 299
RSP_2851 RSP_2851 multidrug (bicyclomycin) efflux pump, Major facilitator superfamily (MFS) (NCBI) 12, 30
RSP_2915 phoR Probable two-component sensor histidine kinase (NCBI) 213, 214
RSP_3004 RSP_3004 Possible Protein kinase (NCBI) 209, 214
RSP_3102 RSP_3102 putative sec-independent protein translocase protein, TatE (NCBI) 214, 306
RSP_3572 galM putative aldose 1-epimerase protein (NCBI) 23, 30
RSP_3593 RSP_3593 hypothetical protein (NCBI) 214, 356
RSP_3665 RSP_3665 transcriptional regulator, LuxR family (NCBI) 214, 384
RSP_3822 RSP_3822 GTP1/OBG family protein (NCBI) 30, 279
RSP_3823 proB1 glutamate 5-kinase (NCBI) 30, 240
RSP_3824 proA Gamma-glutamyl phosphate reductase GPR (NCBI) 30, 101
RSP_4298 RSP_4298 tRNA-Trp (NCBI) 75, 214
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 RSP_2722
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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