Organism : Clostridium acetobutylicum | Module List :
CAC1588

Malolactic regulator, LysR family (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1588
(Mouseover regulator name to see its description)

CAC1588 is regulated by 23 influences and regulates 6 modules.
Regulators for CAC1588 (23)
Regulator Module Operator
CAC0191 366 tf
CAC0201 366 tf
CAC0859 366 tf
CAC1430 366 tf
CAC1588 366 tf
CAC1850 366 tf
CAC2254 366 tf
CAC3443 366 tf
CAC3466 366 tf
CAC3481 366 tf
CAC0195 174 tf
CAC0681 174 tf
CAC0841 174 tf
CAC1430 174 tf
CAC1509 174 tf
CAC1696 174 tf
CAC2616 174 tf
CAC2859 174 tf
CAC2950 174 tf
CAC3143 174 tf
CAC3370 174 tf
CAC3418 174 tf
CAC3481 174 tf

Warning: CAC1588 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
7000 3.00e-03 gttaAGGaGg
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7001 1.70e+03 GGaGTG
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7380 1.20e+02 aaggAGGa.ta
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7381 7.10e+03 GGAGGaAGC
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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 CAC1588

CAC1588 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for CAC1588

CAC1588 has total of 44 gene neighbors in modules 174, 366
Gene neighbors (44)
Gene Common Name Description Module membership
CAC0046 CAC0046 Hypothetical protein, CF-2 family (NCBI ptt file) 264, 366
CAC0179 appD Oligopeptide transport ATP-binding protein (NCBI ptt file) 314, 366
CAC0188 nagA N-acetylglucosamine-6-phosphate deacetylase (gene nagA) (NCBI ptt file) 44, 366
CAC0192 CAC0192 Similar to chloromuconate cycloisomerase (NCBI ptt file) 248, 366
CAC0193 CAC0193 Uncharacterized conserved membrane protein, affecting LPS biosynthesis (NCBI ptt file) 7, 174
CAC0194 CAC0194 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 7, 174
CAC0209 CAC0209 Predicted membrane protein; CF-20 family (NCBI ptt file) 82, 366
CAC0211 bioY BioY protein precursor (NCBI ptt file) 199, 366
CAC0215 CAC0215 Endoglucanase, aminopeptidase M42 family (NCBI ptt file) 22, 366
CAC0281 CAC0281 Molybdate-binding periplasmic protein (NCBI ptt file) 363, 366
CAC0282 CAC0282 Cytosine/guanine deaminase related protein (NCBI ptt file) 283, 366
CAC0444 napA Na/H antiporter (napA) (NCBI ptt file) 62, 174
CAC0467 CAC0467 Uncharacterized membrane protein, homolog of YDAH B.subtilis (NCBI ptt file) 78, 174
CAC0492 CAC0492 Alanine racemase (NCBI ptt file) 174, 318
CAC0547 CAC0547 Lactoylglutation lyase (NCBI ptt file) 346, 366
CAC0668 CAC0668 Predicted membrane protein (NCBI ptt file) 174, 305
CAC0678 CAC0678 CBS domains (NCBI ptt file) 160, 174
CAC0696 CAC0696 Putative altronate dehydratase (NCBI ptt file) 170, 366
CAC0704 CAC0704 Sugar ABC transporter, permease protein (NCBI ptt file) 95, 174
CAC0840 potA Spermidine/putrescine ABC transporter, ATP-binding component (NCBI ptt file) 153, 174
CAC1364 CAC1364 Enzyme from phospholipase D family, possible endonuclease nuc (NCBI ptt file) 204, 366
CAC1468 CAC1468 Predicted acetyltransferase (NCBI ptt file) 174, 315
CAC1552 CAC1552 Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) 44, 366
CAC1588 CAC1588 Malolactic regulator, LysR family (NCBI ptt file) 174, 366
CAC1663 CAC1663 Hypothetical protein (NCBI ptt file) 73, 366
CAC1696 sigG Specialized DNA-dependent RNA polymerase sigma subunit (NCBI ptt file) 174, 235
CAC1842 CAC1842 Uncharacterized protein, B.subtilis YTKC ortholog, related to regulatory protein UTXA (NCBI ptt file) 280, 366
CAC1912 CAC1912 Uncharacterized phage related protein (NCBI ptt file) 121, 366
CAC1939 CAC1939 Hypothetical protein (NCBI ptt file) 54, 366
CAC1968 CAC1968 Pectate lyase related enzyme (NCBI ptt file) 174, 314
CAC2043 CAC2043 Hypothetical protein (NCBI ptt file) 235, 366
CAC2438 CAC2438 Predicted phosphatase (NCBI ptt file) 174, 300
CAC2831 CAC2831 Conserved membrane protein, YccA family (NCBI ptt file) 312, 366
CAC2875 tagO Undecaprenyl-phosphate (NCBI ptt file) 174, 235
CAC2915 panC Pantoate--beta-alanine ligase (NCBI ptt file) 235, 366
CAC2916 panD Aspartate 1-decarboxylase (NCBI ptt file) 235, 366
CAC3032 CAC3032 Galactose mutarotase related enzyme (NCBI ptt file) 174, 315
CAC3220 CAC3220 Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 44, 174
CAC3230 CAC3230 Hydrogenase subunit (ferredoxin) (NCBI ptt file) 174, 330
CAC3357 CAC3357 Hypothetical protein (NCBI ptt file) 118, 174
CAC3377 CAC3377 Xylanase/chitin deacetylase family enzyme (NCBI ptt file) 244, 366
CAC3427 CAC3427 PTS system, (possibly glucose-specific) IIA component (NCBI ptt file) 73, 366
CAC3436 CAC3436 Probable alpha-arabinofuranosidase (NCBI ptt file) 314, 366
CAC3590 CAC3590 Predicted flavoprotein, YhiN family (NCBI ptt file) 174, 301
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 CAC1588
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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