Organism : Clostridium acetobutylicum | Module List :
CAC0559

Transcriptional regulator, MarR/EmrR family (NCBI ptt file)

CircVis
Functional Annotations (4)
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
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0559
(Mouseover regulator name to see its description)

CAC0559 is regulated by 24 influences and regulates 14 modules.
Regulators for CAC0559 (24)
Regulator Module Operator
CAC0081 66 tf
CAC0144 66 tf
CAC0360 66 tf
CAC0393 66 tf
CAC0457 66 tf
CAC0459 66 tf
CAC0559 66 tf
CAC2113 66 tf
CAC2242 66 tf
CAC2473 66 tf
CAC3166 66 tf
CAC3236 66 tf
CAC3349 66 tf
CAC3409 66 tf
CAC3509 66 tf
CAC0197 214 tf
CAC0201 214 tf
CAC0265 214 tf
CAC0559 214 tf
CAC1032 214 tf
CAC2242 214 tf
CAC2297 214 tf
CAC2773 214 tf
CAC3481 214 tf

Warning: CAC0559 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
6786 5.60e-03 aGgAGG
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6787 1.80e+03 GCCTACGC
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7080 2.00e-02 AGGaGg
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7081 8.90e+03 .AtAttGAtaatcATtaTcA
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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 CAC0559

CAC0559 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
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
Module neighborhood information for CAC0559

CAC0559 has total of 37 gene neighbors in modules 66, 214
Gene neighbors (37)
Gene Common Name Description Module membership
CAC0246 CAC0246 Conserved membrane protein, predicted permease (NCBI ptt file) 66, 113
CAC0247 CAC0247 Predicted permease (NCBI ptt file) 66, 356
CAC0267 CAC0267 L-lactate dehydrogenase (NCBI ptt file) 33, 214
CAC0442 CAC0442 Permease, putative chloride channel (NCBI ptt file) 70, 214
CAC0450 CAC0450 Response regulator (CheY-like and HTH domains) (NCBI ptt file) 13, 66
CAC0522 CAC0522 Predicted hydrolase of the HAD superfamily (NCBI ptt file) 66, 282
CAC0559 CAC0559 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 66, 214
CAC0585 CAC0585 N-terminal CheY reciever domain fused to C-terminal uncharacterized CheX-like domain (NCBI ptt file) 66, 151
CAC0587 CAC0587 Flavodoxin (NCBI ptt file) 214, 266
CAC0761 CAC0761 Predicted membrane protein (NCBI ptt file) 66, 86
CAC0778 CAC0778 ATP-dependent RNA helicase, superfamily II (NCBI ptt file) 13, 66
CAC0820 CAC0820 Conserved protein, ortholog YwqG B.subtilis (NCBI ptt file) 13, 66
CAC0885 CAC0885 Ferredoxin 3 fused to uncharacterized domain, orthologous of AF0155 from Archaeoglobus fulgidus (NCBI ptt file) 214, 254
CAC0980 pflB Pyruvate-formate lyase (NCBI ptt file) 214, 218
CAC0981 pflA Pyruvate-formate-lyase-activating enzyme (NCBI ptt file) 214, 218
CAC1029 CAC1029 FeoA-like protein, involved in iron transport (NCBI ptt file) 83, 214
CAC1032 CAC1032 Predicted transcriptional regulator (NCBI ptt file) 83, 214
CAC1334 CAC1334 Fe-S oxidoreductase of MoeA/NarA subfamily (NCBI ptt file) 214, 304
CAC1470 CAC1470 2-Hydroxy-6-Oxo-6-Phenylhexa-2,4-Dienoate hydrolase (NCBI ptt file) 66, 227
CAC1471 arbA Ketopantoate reductase (NCBI ptt file) 66, 227
CAC1478 rpsD Ribosomal protein S4 (NCBI ptt file) 83, 214
CAC1571 CAC1571 Glutathione peroxidase (NCBI ptt file) 70, 214
CAC1590 CAC1590 2-oxoglutarate/malate translocator (NCBI ptt file) 66, 249
CAC1602 CAC1602 Predicted diverged CheY-domain (NCBI ptt file) 196, 214
CAC1655 purQ/purL bifunctional enzyme phosphoribosylformylglycinamidine (FGAM) synthase (synthetase domain/glutamine amidotransferase domain) (NCBI ptt file) 214, 249
CAC2203 hag Possible hook-associated protein, flagellin family (NCBI ptt file) 66, 93
CAC2242 CAC2242 Predicted transcriptional regulator, arsE family (NCBI ptt file) 214, 247
CAC2617 CAC2617 Membrane associated methyl-chemotaxis protein, HAMP domain containing (NCBI ptt file) 66, 360
CAC2820 CAC2820 Predicted permease (NCBI ptt file) 214, 319
CAC2902 CAC2902 Isopentenyl monophosphate kinase, IPK (NCBI ptt file) 66, 247
CAC3334 CAC3334 Multimeric flavodoxin WrbA family protein (NCBI ptt file) 66, 142
CAC3349 CAC3349 Transcriptional regulator, LysR family (NCBI ptt file) 66, 140
CAC3526 CAC3526 FMN-binding protein (NCBI ptt file) 66, 183
CAC3527 CAC3527 Ferredoxin (NCBI ptt file) 66, 249
CAC3552 CAC3552 Lactate dehydrogenase (NCBI ptt file) 214, 218
CAC3567 topB Topoisomerase B (NCBI ptt file) 66, 270
CAC3686 CAC3686 Metallo-beta-lactamase superfamily hydrolase (NCBI ptt file) 33, 66
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 CAC0559
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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