Organism : Clostridium acetobutylicum | Module List :
CAC3154

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

CircVis
Functional Annotations (6)
Function System
rRNA methylases cog/ cog
RNA binding go/ molecular_function
RNA processing go/ biological_process
RNA methyltransferase activity go/ molecular_function
RNA modification go/ biological_process
rRNA_methyl_3 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3154
(Mouseover regulator name to see its description)

CAC3154 is regulated by 24 influences and regulates 0 modules.
Regulators for CAC3154 (24)
Regulator Module Operator
CAC0032 103 tf
CAC0201 103 tf
CAC0255 103 tf
CAC0360 103 tf
CAC0461 103 tf
CAC0863 103 tf
CAC1300 103 tf
CAC1766 103 tf
CAC1800 103 tf
CAC2552 103 tf
CAC3247 103 tf
CAC3267 103 tf
CAC3649 103 tf
CAC0162 19 tf
CAC0255 19 tf
CAC0863 19 tf
CAC0865 19 tf
CAC1320 19 tf
CAC1469 19 tf
CAC1928 19 tf
CAC3267 19 tf
CAC3360 19 tf
CAC3525 19 tf
CAC3606 19 tf

Warning: CAC3154 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
6692 1.20e-07 aGGAGg
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6693 4.10e+02 gtagacggCcT.tcTtctT
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6858 1.10e-01 ctttGGAGG
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6859 2.80e+03 AGAaGtaAgG
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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 CAC3154

CAC3154 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
rRNA methylases cog/ cog
RNA binding go/ molecular_function
RNA processing go/ biological_process
RNA methyltransferase activity go/ molecular_function
RNA modification go/ biological_process
rRNA_methyl_3 tigr/ tigrfam
Module neighborhood information for CAC3154

CAC3154 has total of 36 gene neighbors in modules 19, 103
Gene neighbors (36)
Gene Common Name Description Module membership
CAC0119 cheW Chemotaxis protein cheW (NCBI ptt file) 19, 28
CAC0241 CAC0241 ABC-type multidrug transport system, ATP-ase compoment (NCBI ptt file) 88, 103
CAC0242 CAC0242 Predicted permease (NCBI ptt file) 88, 103
CAC0243 CAC0243 Predicted permease (NCBI ptt file) 88, 103
CAC0674 CAC0674 L-serine dehydratase, alpha chain (NCBI ptt file) 19, 357
CAC0866 CAC0866 ABC-type multidrug transport system, ATPase component (NCBI ptt file) 19, 226
CAC1088 glpX GlpX-like protein (Fructose-1,6-bisphosphatase related protein) (NCBI ptt file) 19, 28
CAC1275 CAC1275 Spore protease (NCBI ptt file) 19, 136
CAC1358 CAC1358 Hypothetical protein (NCBI ptt file) 19, 136
CAC1448 tetP/tetQ tetracycline resistance protein, tetQ family, GTPase (NCBI ptt file) 19, 338
CAC1708 CAC1708 ATPase component of ABC-type phosphate transport system (NCBI ptt file) 103, 245
CAC1709 phoU Phosphate uptake regulator (NCBI ptt file) 103, 111
CAC1952 CAC1952 Hypothetical protein (NCBI ptt file) 19, 343
CAC2365 sspA Small acid-soluble spore protein (NCBI ptt file) 19, 127
CAC2551 CAC2551 RNAse H family protein (NCBI ptt file) 19, 349
CAC2630 CAC2630 Uncharaterized conserved protein, YOME B.subtilis ortholog (NCBI ptt file) 19, 105
CAC2757 CAC2757 Predicted membrane protein (NCBI ptt file) 19, 244
CAC2969 CAC2969 3-methyladenine DNA glycosylase (NCBI ptt file) 19, 127
CAC3007 CAC3007 ATPase component of MDR-type ABC transporter, two ATPase domains (NCBI ptt file) 19, 78
CAC3153 CAC3153 Uncharacterized conserved protein, YACP B.subtilis ortholog (NCBI ptt file) 19, 103
CAC3154 CAC3154 RRNA methylase, YACO B.subtilis ortholog (NCBI ptt file) 19, 103
CAC3155 CAC3155 Uncharacterized conserved protein, THY1 family (NCBI ptt file) 19, 109
CAC3219 CAC3219 Membrane associated histidine kinase with HAMP domain (NCBI ptt file) 19, 63
CAC3309 CAC3309 Predicted membrane protein (NCBI ptt file) 6, 19
CAC3310 CAC3310 Predicted UDP-glucose 6-dehydrogenase (NCBI ptt file) 19, 190
CAC3311 CAC3311 TPR-repeat domain fused to glycosyltransferase (NCBI ptt file) 19, 361
CAC3339 CAC3339 ATPase component of ABC transporter (two ATPase domains) (NCBI ptt file) 88, 103
CAC3340 CAC3340 Uncharacterized conserved domain seen in the bacterial SpoT (NCBI ptt file) 88, 103
CAC3551 natA Na+ ABC transporter (ATP-binding protein), NATA (NCBI ptt file) 19, 88
CAC3559 CAC3559 Uncharacterized conserved membrane protein, YHBJ B.subtilis (possible permease)ortholog (NCBI ptt file) 88, 103
CAC3560 CAC3560 ABC-type transporter, ATPase component (NCBI ptt file) 88, 103
CAC3561 CAC3561 ABC-type transporter, permease component (NCBI ptt file) 88, 103
CAC3582 CAC3582 Hypothetical protein (NCBI ptt file) 98, 103
CAC3583 CAC3583 Predicted permease (NCBI ptt file) 88, 103
CAC3584 CAC3584 Predicted permease (NCBI ptt file) 88, 103
CAC3585 CAC3585 ABC-type transporter, ATPase component (NCBI ptt file) 98, 103
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 CAC3154
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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