Organism : Clostridium acetobutylicum | Module List :
CAC1799 nusA

Transcription terminator NusA (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Transcription elongation factor cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
RNA binding go/ molecular_function
protein binding go/ molecular_function
regulation of transcription termination, DNA-dependent go/ biological_process
NusA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1799
(Mouseover regulator name to see its description)

CAC1799 is regulated by 21 influences and regulates 17 modules.
Regulators for CAC1799 nusA (21)
Regulator Module Operator
CAC0856 310 tf
CAC1032 310 tf
CAC1682 310 tf
CAC1753 310 tf
CAC1786 310 tf
CAC1799 310 tf
CAC1800 310 tf
CAC2430 310 tf
CAC2842 310 tf
CAC3409 310 tf
CAC0459 213 tf
CAC0559 213 tf
CAC0821 213 tf
CAC0860 213 tf
CAC1264 213 tf
CAC1300 213 tf
CAC1799 213 tf
CAC1800 213 tf
CAC2074 213 tf
CAC2143 213 tf
CAC2306 213 tf

Warning: CAC1799 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
7078 1.30e-01 GGAGgG
Loader icon
7079 1.10e+02 caAt.aaaGtgctT..TtgC.
Loader icon
7272 1.00e-02 AGGAGgga
Loader icon
7273 2.50e+03 AAGAgaGTGg
Loader icon
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 CAC1799

CAC1799 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcription elongation factor cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
RNA binding go/ molecular_function
protein binding go/ molecular_function
regulation of transcription termination, DNA-dependent go/ biological_process
NusA tigr/ tigrfam
Module neighborhood information for CAC1799

CAC1799 has total of 31 gene neighbors in modules 213, 310
Gene neighbors (31)
Gene Common Name Description Module membership
CAC1026 CAC1026 Superfamily I DNA helicase (NCBI ptt file) 213, 315
CAC1726 CAC1726 Predicted Fe-S-cluster redox enzyme, YLON B.subtilis ortholog (NCBI ptt file) 213, 329
CAC1729 CAC1729 Predicted GTPase (YLOQ B.subtilis ortholog) (NCBI ptt file) 213, 315
CAC1751 smc Chromosome segregation SMC protein, ATPase (NCBI ptt file) 213, 269
CAC1788 tsf Translation elongation factor Ts (NCBI ptt file) 237, 310
CAC1789 smbA/pyrH Uridylate kinase (NCBI ptt file) 310, 360
CAC1790 frr Ribosome recycling factor (NCBI ptt file) 310, 315
CAC1798 CAC1798 Uncharacterized protein, YhbC family (NCBI ptt file) 213, 310
CAC1799 nusA Transcription terminator NusA (NCBI ptt file) 213, 310
CAC1800 CAC1800 Uncharacterized conserved protein, YLXR B.subtilis homolog (NCBI ptt file) 213, 310
CAC1801 CAC1801 Possibly nucleic acid binding protein similar to ribosomal protein HS6-type, YLXQ B.subtilis ortholog (NCBI ptt file) 213, 310
CAC1802 infB Translation IF2, GTPase (NCBI ptt file) 14, 213
CAC1803 rfbA Ribosome-binding factor A (NCBI ptt file) 213, 310
CAC1804 CAC1804 Exopolyphosphatase family protein (NCBI ptt file) 5, 213
CAC1805 truB Pseudouridine synthase (NCBI ptt file) 213, 310
CAC1806 CAC1806 Riboflavin kinase/FAD synthase (NCBI ptt file) 5, 213
CAC1809 CAC1809 Uncharacterized conserved protein, YLMC B.subtilis ortholog (NCBI ptt file) 213, 274
CAC1810 dapG Aspartokinase (NCBI ptt file) 213, 274
CAC2081 xseB Exonuclease VII small subunit (NCBI ptt file) 159, 310
CAC2083 folD Tetrahydrofolate dehydrogenase/cyclohydrolase, FolD (NCBI ptt file) 84, 310
CAC2372 sspA Small acid-soluble spore protein (NCBI ptt file) 163, 310
CAC2626 fabG Possible 3-ketoacyl-acyl carrier protein reductase (NCBI ptt file) 310, 360
CAC2627 CAC2627 Predicted S-adenosylmethionine-dependent methyltransferase, YtmQ B.subtilis ortholog (NCBI ptt file) 310, 360
CAC2628 CAC2628 Predicted metal-dependent peptidase (NCBI ptt file) 310, 360
CAC2629 CAC2629 Hypothetical secreted protein (NCBI ptt file) 36, 310
CAC2632 CAC2632 Hypothetical protein (NCBI ptt file) 310, 329
CAC2842 CAC2842 Transcription accessory protein TEX, RNA-binding protein containing S1 domain (NCBI ptt file) 105, 310
CAC2879 upp Uracil phosphoribosyltransferase (NCBI ptt file) 28, 310
CAC2884 prfA Protein chain release factor A (NCBI ptt file) 213, 229
CAC2894 CAC2894 Uncharacterized protein, ywiB B.subtilis homolog (NCBI ptt file) 84, 310
CAC2895 ddlA D-alanine-D-alanine ligase (NCBI ptt file) 310, 329
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 CAC1799
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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