Organism : Clostridium acetobutylicum | Module List :
CAC2358

RRNA methylase, YSGA B.subtilis ortholog (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
rRNA methylases cog/ cog
RNA binding go/ molecular_function
RNA processing go/ biological_process
RNA methyltransferase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2358
(Mouseover regulator name to see its description)

CAC2358 is regulated by 26 influences and regulates 0 modules.
Regulators for CAC2358 (26)
Regulator Module Operator
CAC0289 353 tf
CAC0571 353 tf
CAC0681 353 tf
CAC0723 353 tf
CAC0766 353 tf
CAC0841 353 tf
CAC1465 353 tf
CAC1467 353 tf
CAC2254 353 tf
CAC3199 353 tf
CAC3399 353 tf
CAC3438 353 tf
CAC3502 353 tf
CAC0461 84 tf
CAC0856 84 tf
CAC0933 84 tf
CAC1032 84 tf
CAC1086 84 tf
CAC1753 84 tf
CAC1786 84 tf
CAC1799 84 tf
CAC2084 84 tf
CAC2842 84 tf
CAC3143 84 tf
CAC3149 84 tf
CAC3192 84 tf

Warning: CAC2358 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
6822 8.60e-03 AGGAaG
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6823 1.10e+04 GCacGAGG
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7358 1.40e+01 TTGaAggGaaG
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7359 1.80e+02 gAGaAacGGC
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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 CAC2358

CAC2358 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
rRNA methylases cog/ cog
RNA binding go/ molecular_function
RNA processing go/ biological_process
RNA methyltransferase activity go/ molecular_function
Module neighborhood information for CAC2358

CAC2358 has total of 46 gene neighbors in modules 84, 353
Gene neighbors (46)
Gene Common Name Description Module membership
CAC0027 pyrE Orotate phosphoribosyltranspherase (NCBI ptt file) 84, 254
CAC0035 CAC0035 Serine/threonine phosphatase (inactivated protein) (NCBI ptt file) 236, 353
CAC0037 CAC0037 MinD family ATPase from ParA/SOJ subfamily (NCBI ptt file) 264, 353
CAC0066 CAC0066 ABC transporter, ATP-binding protein (NCBI ptt file) 28, 353
CAC0158 glmS Glucoseamine-fructose-6-phosphate aminotransferase (gene glmS) (NCBI ptt file) 36, 84
CAC0306 CAC0306 SAM-dependent methyltransferase (NCBI ptt file) 217, 353
CAC0436 CAC0436 Predicted xylanase/chitin deacetilase, similar to yxkH B.subtilis (NCBI ptt file) 320, 353
CAC0530 CAC0530 Hypothetical protein (NCBI ptt file) 102, 353
CAC0571 CAC0571 Predicted transcriptional regulator (NCBI ptt file) 191, 353
CAC0572 CAC0572 Predicted membrane protein (NCBI ptt file) 191, 353
CAC0652 CAC0652 Uncharacterized conserved membrane protein, similar to MDR (VANZ) ORF of Enterococcus (NCBI ptt file) 246, 353
CAC0752 CAC0752 Homolog of eukaryotic DNA ligase III (NCBI ptt file) 327, 353
CAC0753 CAC0753 PolyA polymerase related protein (HD hydrolase) and P-loop ATP-ase domain (NCBI ptt file) 137, 353
CAC0754 CAC0754 Hypothetical protein (NCBI ptt file) 165, 353
CAC0802 CAC0802 Hypothetical protein (NCBI ptt file) 212, 353
CAC0883 CAC0883 Probable cation efflux pump (multidrug resistance protein) (NCBI ptt file) 84, 254
CAC0944 tkt Transketolase (NCBI ptt file) 84, 292
CAC1255 CAC1255 Uncharacterized conserved protein (NCBI ptt file) 84, 254
CAC1256 CAC1256 Ribonucleases G/E family protein (NCBI ptt file) 84, 258
CAC1278 lepA Membrane GTPase lepA (NCBI ptt file) 84, 254
CAC1295 CAC1295 ERA GTPase (NCBI ptt file) 64, 84
CAC1712 gpsA Glycerol 3-phosphate dehydrogenase (NCBI ptt file) 84, 350
CAC2083 folD Tetrahydrofolate dehydrogenase/cyclohydrolase, FolD (NCBI ptt file) 84, 310
CAC2317 tagA Teichoic acid biosynthesis protein, tagA (NCBI ptt file) 84, 211
CAC2358 CAC2358 RRNA methylase, YSGA B.subtilis ortholog (NCBI ptt file) 84, 353
CAC2373 CAC2373 Predicted membrane protein (NCBI ptt file) 76, 84
CAC2401 CAC2401 Activator of 2-hydroxyglutaryl-CoA dehydratase (duplicated HSP70 class ATPase domain) fused to uncharacterized conserved protein (NCBI ptt file) 28, 84
CAC2697 CAC2697 Hypothetical protein (NCBI ptt file) 306, 353
CAC2740 hisS Histidyl-tRNA synthetase (NCBI ptt file) 84, 324
CAC2850 CAC2850 Proline/glycine betaine ABC-type transport system, ATPase component (NCBI ptt file) 8, 84
CAC2894 CAC2894 Uncharacterized protein, ywiB B.subtilis homolog (NCBI ptt file) 84, 310
CAC2948 CAC2948 ATPase components of ABC transporter with duplicated ATPase domains (second domain is inactivated) (NCBI ptt file) 79, 84
CAC2983 CAC2983 Hypothetical protein (NCBI ptt file) 84, 350
CAC3010 CAC3010 ATP-dependent RNA helicase (superfamily II), YDBR B.subtilis ortholog (NCBI ptt file) 84, 106
CAC3012 CAC3012 ATPase component of ABC transporter, with duplicated ATPase domains (NCBI ptt file) 44, 84
CAC3095 thiK Hydroxyethylthiazole kinase ThiM/ThiK (FS!) (NCBI ptt file) 353, 360
CAC3100 CAC3100 Predicted permease (Cobalt permease subfamily) (NCBI ptt file) 84, 106
CAC3156 CAC3156 Uncharacterized conserved protein, YACZ B.subtilis ortholog (NCBI ptt file) 84, 324
CAC3281 CAC3281 ABC-type multidrug/protein/lipid transport system, ATPase component (NCBI ptt file) 84, 324
CAC3331 CAC3331 Alanine racemase (NCBI ptt file) 24, 353
CAC3430 CAC3430 Membrane associated, signal transduction histidine kinase-like ATPase (NCBI ptt file) 4, 353
CAC3440 CAC3440 Hypothetical protein (NCBI ptt file) 353, 360
CAC3441 CAC3441 DNA/RNA helicase, SNF2 (NCBI ptt file) 28, 353
CAC3442 polC DNA polymerase III (alpha subunit) (NCBI ptt file) 28, 353
CAC3476 CAC3476 Methyl-accepting chemotaxis protein (NCBI ptt file) 208, 353
CAC3721 CAC3721 Hypothetical secreted protein (NCBI ptt file) 84, 324
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 CAC2358
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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