Organism : Clostridium acetobutylicum | Module List :
CAC0745

Transcriptional 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 CAC0745
(Mouseover regulator name to see its description)

CAC0745 is regulated by 23 influences and regulates 9 modules.
Regulators for CAC0745 (23)
Regulator Module Operator
CAC0113 71 tf
CAC0382 71 tf
CAC0465 71 tf
CAC0723 71 tf
CAC0745 71 tf
CAC0856 71 tf
CAC1404 71 tf
CAC2568 71 tf
CAC2851 71 tf
CAC3142 71 tf
CAC3611 71 tf
CAC3651 71 tf
CAC3729 71 tf
CAC0162 83 tf
CAC0393 83 tf
CAC0559 83 tf
CAC0745 83 tf
CAC1032 83 tf
CAC1670 83 tf
CAC1675 83 tf
CAC1695 83 tf
CAC2552 83 tf
CAC3143 83 tf

Warning: CAC0745 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
6796 1.10e-04 AGGaGag
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6797 8.60e+03 GGcaAGTTTGCTC
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6820 5.30e-02 TttCCtCC
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6821 2.10e+02 tAg.gtAAa.atagt
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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 CAC0745

CAC0745 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 CAC0745

CAC0745 has total of 45 gene neighbors in modules 71, 83
Gene neighbors (45)
Gene Common Name Description Module membership
CAC0055 CAC0055 Uncharacterized predicted metal-binding protein, ortholog of Streptomyces (2808777) (NCBI ptt file) 71, 185
CAC0162 CAC0162 Transcriptional regulator MarR/EmrR family (NCBI ptt file) 83, 276
CAC0371 CAC0371 Response regulator (CheY-like domain and HTH domain) (NCBI ptt file) 71, 287
CAC0394 kdgA Deoxyphosphogluconate aldolase (gene kdgA) (NCBI ptt file) 83, 326
CAC0417 CAC0417 Similar to arsenate reductase (NCBI ptt file) 71, 185
CAC0536 dltE Short-chain dehydrodenase (gene dltE) (NCBI ptt file) 71, 108
CAC0560 CAC0560 Integral membrane protein similar to antibiotic resistance protein B.subtilis (NCBI ptt file) 83, 165
CAC0594 CAC0594 Predicted phosphate-utilizing enzyme involved in pyridoxine/purine/histidine biosynthesis (NCBI ptt file) 83, 266
CAC0595 CAC0595 Glutamine amidotranspherase (possibly involved in histidine and purine biosinthesis) (NCBI ptt file) 83, 291
CAC0600 CAC0600 Predicted membrane protein (NCBI ptt file) 10, 71
CAC0669 CAC0669 Hypothetical protein (NCBI ptt file) 83, 266
CAC0718 CAC0718 Ortholog ycnD B.subtilis, nitroreductase (NCBI ptt file) 83, 326
CAC0745 CAC0745 Transcriptional regulator, LysR family (NCBI ptt file) 71, 83
CAC0858 CAC0858 Phosphinothricin acetyltransferase (NCBI ptt file) 71, 216
CAC1029 CAC1029 FeoA-like protein, involved in iron transport (NCBI ptt file) 83, 214
CAC1030 CAC1030 FeoA-like protein, involved in iron transport (NCBI ptt file) 83, 266
CAC1031 feoB FeoB-like GTPase, responsible for iron uptake (NCBI ptt file) 80, 83
CAC1032 CAC1032 Predicted transcriptional regulator (NCBI ptt file) 83, 214
CAC1046 CAC1046 Transcriptional regulator, LysR family (NCBI ptt file) 71, 287
CAC1478 rpsD Ribosomal protein S4 (NCBI ptt file) 83, 214
CAC1493 CAC1493 Zn-finger DNA-binding domain (NCBI ptt file) 71, 74
CAC1496 CAC1496 Uncharacterized protein, homolog of YCGL B.subtilis (NCBI ptt file) 71, 137
CAC1502 CAC1502 Hypothetical protein (NCBI ptt file) 71, 346
CAC1540 CAC1540 Uncharacterized ATP-grasp enzyme (NCBI ptt file) 71, 91
CAC1549 bsaA Glutathione peroxidase (NCBI ptt file) 83, 266
CAC1577 CAC1577 Ncharacterized conserved protein (NCBI ptt file) 71, 239
CAC1603 CAC1603 Diverged enzyme related to 2'-5' RNA ligase, ortholog YJCG B.subtilis (NCBI ptt file) 70, 83
CAC1618 CAC1618 Hypothetical protein (NCBI ptt file) 71, 132
CAC1619 CAC1619 Hypothetical protein (NCBI ptt file) 71, 259
CAC1621 CAC1621 Predicted Fe-S oxidoreductase (NCBI ptt file) 71, 261
CAC1675 CAC1675 Predicted transcriptional regulator (HTH winged helix type) (NCBI ptt file) 31, 83
CAC1962 CAC1962 Predicted esterase of alpha/beta hydrolase superfamily, YBBA B.subtilis ortholog (NCBI ptt file) 71, 72
CAC2520 CAC2520 Multimeric flavodoxin (WrbA) domain containing protein (NCBI ptt file) 49, 71
CAC2568 CAC2568 Predicted transcriptional regulator (NCBI ptt file) 71, 223
CAC2684 CAC2684 Sugar kinase, ribokinase family (NCBI ptt file) 83, 326
CAC2734 CAC2734 ABC-type multidrug transport system, ATPase component (NCBI ptt file) 71, 98
CAC2759 CAC2759 Response regulator (CheY receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 71, 185
CAC2930 CAC2930 Uncharacterized conserved membrane protein (NCBI ptt file) 71, 223
CAC2931 CAC2931 Uncharacterized conserved membrane protein (NCBI ptt file) 71, 223
CAC3303 CAC3303 Superfamily II DNA/RNA helicases, SNF2 family (NCBI ptt file) 71, 294
CAC3387 CAC3387 Pectate lyase (NCBI ptt file) 83, 261
CAC3503 CAC3503 Nucleoside-diphosphate-sugar epimerase (NCBI ptt file) 83, 240
CAC3529 CAC3529 Hypothetical protein (NCBI ptt file) 71, 259
CAC3530 CAC3530 Hypothetical protein (NCBI ptt file) 71, 259
CAC3607 CAC3607 Possible ketopantoate reductase PanE/ApbA (NCBI ptt file) 83, 216
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 CAC0745
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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