Organism : Clostridium acetobutylicum | Module List :
CAC2399 vals

Valyl-tRNA synthetase (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Valyl-tRNA synthetase cog/ cog
valine-tRNA ligase activity go/ molecular_function
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
valyl-tRNA aminoacylation go/ biological_process
valS tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2399
(Mouseover regulator name to see its description)

CAC2399 is regulated by 24 influences and regulates 0 modules.
Regulators for CAC2399 vals (24)
Regulator Module Operator
CAC0019 297 tf
CAC0144 297 tf
CAC0255 297 tf
CAC0265 297 tf
CAC0284 297 tf
CAC0707 297 tf
CAC0766 297 tf
CAC1333 297 tf
CAC1928 297 tf
CAC2074 297 tf
CAC2113 297 tf
CAC2476 297 tf
CAC3143 297 tf
CAC3149 297 tf
CAC0155 296 tf
CAC0183 296 tf
CAC0465 296 tf
CAC0569 296 tf
CAC0768 296 tf
CAC0849 296 tf
CAC2084 296 tf
CAC2793 296 tf
CAC3037 296 tf
CAC3216 296 tf

Warning: CAC2399 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
7244 1.70e-03 TttTTAGGaGG
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7245 4.50e-01 gtGgTaccGcG
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7246 8.40e+01 aGGagG
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7247 1.20e+03 ggGtatagcgtTTcTAtC
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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 CAC2399

CAC2399 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Valyl-tRNA synthetase cog/ cog
valine-tRNA ligase activity go/ molecular_function
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
valyl-tRNA aminoacylation go/ biological_process
valS tigr/ tigrfam
Module neighborhood information for CAC2399

CAC2399 has total of 37 gene neighbors in modules 296, 297
Gene neighbors (37)
Gene Common Name Description Module membership
CAC0077 CAC0077 Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file) 297, 317
CAC0617 CAC0617 Hypothetical protein, CF-25 family (NCBI ptt file) 58, 296
CAC0626 trpS Tryptophan-tRNA synthetase, trpS (NCBI ptt file) 247, 296
CAC0682 nrgA Ammonium transporter (membrane protein nrgA) (NCBI ptt file) 8, 297
CAC0744 CAC0744 Na+/H+ antiporter, ortholog YQKI B.subtilis (NCBI ptt file) 252, 297
CAC0768 CAC0768 Transcriptional regulator, LysR family (NCBI ptt file) 58, 296
CAC1041 argS Arginyl-tRNA synthetase (NCBI ptt file) 147, 296
CAC1042 CAC1042 Predicted membrane protein (NCBI ptt file) 149, 296
CAC1097 CAC1097 Hypothetical protein (NCBI ptt file) 297, 317
CAC1235 thrB Homoserine kinase (thrB) (NCBI ptt file) 58, 296
CAC1267 dacB D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 218, 296
CAC1307 CAC1307 Hypothetical protein (NCBI ptt file) 51, 297
CAC1611 CAC1611 Probable cation efflux pump (multidrug resistance protein) (NCBI ptt file) 8, 297
CAC1757 CAC1757 RimM protein, required for 16S rRNA processing (NCBI ptt file) 76, 297
CAC1758 trmD TRNA-(guanine-N1)-methyltransferase, TrmD (NCBI ptt file) 76, 297
CAC1821 purB Adenylosuccinate lyase (NCBI ptt file) 106, 297
CAC2265 CAC2265 Uncharacterized conserved membrane protein (NCBI ptt file) 106, 297
CAC2266 CAC2266 Uncharacterized conserved membrane protein (fragment) (NCBI ptt file) 106, 297
CAC2295 CAC2295 Uncharacterized conserved protein, YebC family (NCBI ptt file) 152, 296
CAC2367 CAC2367 Uncharacterized protein containing predicted cell adhesion domain and ChW-repeats (NCBI ptt file) 77, 296
CAC2374 oppC Oligopeptide ABC-type transporter, permease component OPPC (NCBI ptt file) 224, 297
CAC2375 oppB Oligopeptide ABC-type transporter, permease (NCBI ptt file) 224, 297
CAC2397 CAC2397 Hypothetical protein (NCBI ptt file) 106, 296
CAC2398 folC Folylpolyglutamate synthase (NCBI ptt file) 296, 297
CAC2399 vals Valyl-tRNA synthetase (NCBI ptt file) 296, 297
CAC2649 CAC2649 Uncharacterized conserved membrane protein (NCBI ptt file) 237, 296
CAC2656 CAC2656 Protein containing uncharacterized domain from NimC family (NCBI ptt file) 59, 296
CAC2657 CAC2657 Polyferredoxin (NCBI ptt file) 59, 296
CAC2849 CAC2849 Proline/glycine betaine ABC-type transport system, permease component fused to periplasmic component (NCBI ptt file) 8, 297
CAC2925 CAC2925 HD superfamily hydrolase (NCBI ptt file) 286, 297
CAC2926 sul Dihydropteroate synthase (NCBI ptt file) 34, 297
CAC2927 folA/folK Dihydroneopterin aldolase fused to 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (NCBI ptt file) 286, 297
CAC3262 CAC3262 ATPase with chaperone activity, ATP-binding domain, diverged (NCBI ptt file) 224, 297
CAC3288 CAC3288 Iron-regulated ABC transporter ATPase subunit (SufC), VEG296 B.subtilis ortholog (NCBI ptt file) 201, 296
CAC3291 CAC3291 Selenocysteine lyase, NifS family (NCBI ptt file) 209, 296
CAC3390 CAC3390 Response regulator (CheY-like receiver domain containing) (NCBI ptt file) 51, 297
CAC3728 CAC3728 Hypothetical protein (NCBI ptt file) 132, 296
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 CAC2399
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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