Organism : Clostridium acetobutylicum | Module List :
CAC1467

Transcriptional regulator, Lrp family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1467
(Mouseover regulator name to see its description)

CAC1467 is regulated by 19 influences and regulates 40 modules.
Regulators for CAC1467 (19)
Regulator Module Operator
CAC0078 178 tf
CAC0289 178 tf
CAC1467 178 tf
CAC2306 178 tf
CAC3409 178 tf
CAC3729 178 tf
CAC0768 278 tf
CAC0860 278 tf
CAC0951 278 tf
CAC1670 278 tf
CAC1695 278 tf
CAC2084 278 tf
CAC2306 278 tf
CAC2307 278 tf
CAC2471 278 tf
CAC2768 278 tf
CAC3216 278 tf
CAC3443 278 tf
CAC3673 278 tf

Warning: CAC1467 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
7008 8.70e-02 AGGgGg
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7009 8.90e+01 aca.CatTttAcAtt.atTgcg
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7208 2.70e-05 aaGgggGa
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7209 4.60e+04 aCGGGA
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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 CAC1467

CAC1467 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for CAC1467

CAC1467 has total of 35 gene neighbors in modules 178, 278
Gene neighbors (35)
Gene Common Name Description Module membership
CAC0003 CAC0003 Small conserved protein, ortholog of YAAA B.subtilis (NCBI ptt file) 105, 278
CAC0007 gyrA DNA gyrase (topoisomerase II) A subunit (NCBI ptt file) 29, 278
CAC0078 agrB Accessory gene regulator protein B (NCBI ptt file) 7, 178
CAC0082 CAC0082 Predicted membrane protein (NCBI ptt file) 178, 292
CAC0111 CAC0111 Glutamine-binding periplasmic protein fused to glutamine permease (NCBI ptt file) 106, 278
CAC0178 appC Oligopeptide transport permease protein (NCBI ptt file) 278, 314
CAC0180 appF Oligopeptide ABC transporter, ATP-binding protein (NCBI ptt file) 179, 278
CAC0627 CAC0627 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 278, 283
CAC0655 CAC0655 Hypothetical protein, CF-26 family (NCBI ptt file) 278, 318
CAC0702 CAC0702 Predicted lipoprotein, Med/BMP family (NCBI ptt file) 58, 278
CAC0714 secG Membrane protein secG involved in protein secretion (NCBI ptt file) 25, 278
CAC0792 CAC0792 D-amino acid aminotransferase (NCBI ptt file) 7, 178
CAC1010 CAC1010 Predicted phosphohydrolase, Icc family (NCBI ptt file) 155, 178
CAC1314 CAC1314 Hypothetical protein (NCBI ptt file) 18, 178
CAC1315 CAC1315 Peptodoglycan-binding domain containing protein (NCBI ptt file) 18, 178
CAC1453 rbsB Ribose ABC transporter (ribose-binding periplasmic component) (NCBI ptt file) 235, 278
CAC1467 CAC1467 Transcriptional regulator, Lrp family (NCBI ptt file) 178, 278
CAC1542 CAC1542 Predicted membrane protein (NCBI ptt file) 278, 283
CAC1731 CAC1731 Predicted nucleotide-binding protein, YLOS B.subtilis ortholog (NCBI ptt file) 2, 278
CAC1750 CAC1750 SpoVS-related protein (NCBI ptt file) 29, 278
CAC2261 CAC2261 HD-hydrolase domain containing protein, YHAM B.subtilis ortholog (NCBI ptt file) 38, 278
CAC2306 CAC2306 Sporulation-specific sigma factor F (NCBI ptt file) 164, 278
CAC2307 CAC2307 Sigma factor F inhibitor spoIIAB (anti-sigma factor) (NCBI ptt file) 164, 278
CAC2321 CAC2321 Predicted glycosyltransferase (NCBI ptt file) 63, 278
CAC2382 ssb Single-strand DNA-binding protein, ssb (NCBI ptt file) 18, 178
CAC2581 CAC2581 6-pyruvoyl-tetrahydropterin synthase related domain; conserved membrane protein (NCBI ptt file) 18, 178
CAC2635 CAC2635 Hypothetical protein (NCBI ptt file) 80, 278
CAC2695 CAC2695 Diverged Metallo-dependent hydrolase(Zn) of DD-Peptidase family; peptodoglycan-binding domain (NCBI ptt file) 60, 178
CAC2724 CAC2724 Hypothetical protein (NCBI ptt file) 51, 278
CAC2727 CAC2727 Predicted PHP family hydrolase (NCBI ptt file) 53, 278
CAC2854 recD ATP-dependent exoDNAse (exonuclease V), alpha subunit, RecD (NCBI ptt file) 278, 286
CAC3355 CAC3355 Polyketide synthase pksE (short-chain alcohol dehydrogenase,acyl-carrier-protein S-malonyltransferase,3-oxoacyl-(acyl-carrier-protein) synthase I domains) (NCBI ptt file) 7, 178
CAC3408 CAC3408 NADH oxidase (two distinct flavin oxidoreductase domains) (NCBI ptt file) 7, 178
CAC3409 alsR Transcriptional regulators, LysR family (NCBI ptt file) 7, 178
CAC3423 CAC3423 Acetyltransferase (ribosomal protein N-acetylase subfamily) (NCBI ptt file) 18, 178
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 CAC1467
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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