Organism : Clostridium acetobutylicum | Module List :
CAC3418

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

CircVis
Functional Annotations (6)
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
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3418
(Mouseover regulator name to see its description)

CAC3418 is regulated by 26 influences and regulates 15 modules.
Regulators for CAC3418 (26)
Regulator Module Operator
CAC0078 289 tf
CAC0081 289 tf
CAC0299 289 tf
CAC0402 289 tf
CAC0681 289 tf
CAC1280 289 tf
CAC1668 289 tf
CAC1682 289 tf
CAC2071 289 tf
CAC2473 289 tf
CAC2842 289 tf
CAC2889 289 tf
CAC3152 289 tf
CAC3418 289 tf
CAC0459 239 tf
CAC0474 239 tf
CAC0951 239 tf
CAC1945 239 tf
CAC2071 239 tf
CAC2471 239 tf
CAC2473 239 tf
CAC2889 239 tf
CAC3224 239 tf
CAC3418 239 tf
CAC3579 239 tf
CAC3611 239 tf
Regulated by CAC3418 (15)
Module Residual Genes
23 0.36 20
30 0.33 20
62 0.40 26
73 0.43 28
80 0.37 24
109 0.43 27
123 0.59 24
126 0.31 15
174 0.37 20
239 0.43 21
249 0.38 21
289 0.41 20
292 0.41 24
315 0.39 24
327 0.35 18
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
7130 2.20e-03 AAGgaGGta
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7131 3.00e+01 GagGTGAt
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7230 3.50e-08 agGaGGtg
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7231 1.70e+02 CcCtGccC
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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 CAC3418

CAC3418 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
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
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for CAC3418

CAC3418 has total of 38 gene neighbors in modules 239, 289
Gene neighbors (38)
Gene Common Name Description Module membership
CAC0033 CAC0033 ABC1 family protein kinase (NCBI ptt file) 87, 239
CAC0327 CAC0327 Bacterioferritin comigratory protein (AHPC/TSA family) (NCBI ptt file) 239, 325
CAC0482 CAC0482 Zn-dependent hydrolases of the metallo-beta-lactamase superfamily (NCBI ptt file) 225, 239
CAC0537 CAC0537 Acetylxylan esterase, acyl-CoA esterase or GDSL lipase family, strong similarity to C-terminal region of endoglucanase E precursor (NCBI ptt file) 289, 325
CAC0636 CAC0636 Signal transduction protein containing diguanilate cyclase/phosphodiesterase domain (GGDEF) (NCBI ptt file) 87, 239
CAC1287 CAC1287 HIT family hydrolase (NCBI ptt file) 128, 289
CAC1449 CAC1449 Hypothetical protein (NCBI ptt file) 239, 356
CAC1479 ilvE Branched-chain-amino-acid transaminase (ilvE) (NCBI ptt file) 87, 289
CAC1577 CAC1577 Ncharacterized conserved protein (NCBI ptt file) 71, 239
CAC1680 CAC1680 Predicted endonuclease involved in recombination (NCBI ptt file) 87, 289
CAC1681 CAC1681 Hypothetical protein (NCBI ptt file) 239, 289
CAC1682 CAC1682 Ferric uptake regulation protein (NCBI ptt file) 128, 289
CAC1683 CAC1683 Predicted metal-dependent hydrolase of metallo-beta-lactamase superfamily (NCBI ptt file) 239, 276
CAC1795 CAC1795 1-deoxy-D-xylulose 5-phosphate reductoisomerase (NCBI ptt file) 87, 239
CAC1958 CAC1958 Predicted aldo/keto reductase, YTBE/YVGN B.subtilis ortholog (NCBI ptt file) 128, 289
CAC2071 CAC2071 Spo0A protein, (CheY-like receiver domain and HTH-type DNA binding domain) (NCBI ptt file) 128, 289
CAC2116 CAC2116 General stress protein, DnaK suppressor DskA, YTEA B.subtilis ortholog (NCBI ptt file) 239, 283
CAC2117 pfs Nucleoside phosphorylase (NCBI ptt file) 239, 286
CAC2131 CAC2131 Hypothetical protein (NCBI ptt file) 239, 289
CAC2132 CAC2132 Predicted S-adenosylmethionine-dependent methyltransferase, involved in cell envelope biogenesis YLXA B.subtilis ortholog (NCBI ptt file) 201, 239
CAC2301 mrcB Membrane carboxypeptidase mrcB (NCBI ptt file) 239, 345
CAC2332 spsJ DTDP-D-glucose 4,6-dehydratase (NCBI ptt file) 20, 239
CAC2334 CAC2334 UDP-glucose 4-epimerase (NCBI ptt file) 128, 289
CAC2335 CAC2335 UTP-glucose-1-phosphate uridylyltransferase (NCBI ptt file) 128, 289
CAC2385 CAC2385 Hypothetical protein (NCBI ptt file) 289, 295
CAC2415 CAC2415 Uncharacterized conserved protein (NCBI ptt file) 91, 289
CAC2452 CAC2452 Flavodoxin (NCBI ptt file) 289, 325
CAC2640 clpP Protease subunits of ATP-dependent protease, ClpP (NCBI ptt file) 128, 289
CAC2647 CAC2647 Diverged arginase family hydrolase (NCBI ptt file) 201, 289
CAC2789 CAC2789 Hypothetical protein (NCBI ptt file) 73, 289
CAC2889 rho Transcription termination factor rho (NCBI ptt file) 20, 239
CAC3223 spoVG Stage V sporulation protein G (NCBI ptt file) 105, 289
CAC3231 CAC3231 Predicted phosphatase, HAD superfamily (NCBI ptt file) 239, 295
CAC3418 CAC3418 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 239, 289
CAC3569 accD Acetyl-CoA carboxylase beta subunit (NCBI ptt file) 182, 239
CAC3581 CAC3581 HAD superfamily hydrolase (NCBI ptt file) 185, 289
CAC3632 oppA Oligopeptide ABC transporter, periplasmic substrate-binding component (NCBI ptt file) 87, 239
CAC3657 CAC3657 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (NCBI ptt file) 239, 283
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 CAC3418
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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