Organism : Clostridium acetobutylicum | Module List :
CAC2297

Transcriptional regulator of MocR family (DNA-binding HTH domain and aminotransferase domain) (NCBI ptt file)

CircVis
Functional Annotations (11)
Function System
Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs cog/ cog
adenyl-nucleotide exchange factor activity go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
protein folding go/ biological_process
biosynthetic process go/ biological_process
transferase activity, transferring nitrogenous groups go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
protein homodimerization activity go/ molecular_function
chaperone binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2297
(Mouseover regulator name to see its description)

CAC2297 is regulated by 22 influences and regulates 6 modules.
Regulators for CAC2297 (22)
Regulator Module Operator
CAC2143 91 tf
CAC2297 91 tf
CAC2476 91 tf
CAC3166 91 tf
CAC3361 91 tf
CAC3729 91 tf
CAC0081 3 tf
CAC0113 3 tf
CAC0201 3 tf
CAC0859 3 tf
CAC1786 3 tf
CAC1799 3 tf
CAC2060 3 tf
CAC2074 3 tf
CAC2084 3 tf
CAC2209 3 tf
CAC2297 3 tf
CAC2939 3 tf
CAC3063 3 tf
CAC3152 3 tf
CAC3166 3 tf
CAC3472 3 tf

Warning: CAC2297 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
6660 5.00e-04 AGGAgGaa
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6661 6.90e+03 CCaTGGTTTcCC
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6836 7.00e-06 AGGagggg
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6837 7.90e+03 CTaGCCaCC
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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 CAC2297

CAC2297 is enriched for 11 functions in 3 categories.
Module neighborhood information for CAC2297

CAC2297 has total of 48 gene neighbors in modules 3, 91
Gene neighbors (48)
Gene Common Name Description Module membership
CAC0001 dnaA DNA replication initiator protein, ATPase (NCBI ptt file) 3, 5
CAC0002 dnaN DNA polymerase III beta subunit (NCBI ptt file) 3, 283
CAC0224 CAC0224 Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) 3, 91
CAC0229 CAC0229 Predicted Zn-dependent proteases, TLDD ortholog (NCBI ptt file) 91, 225
CAC0230 CAC0230 Inactivated predicted Zn-dependent protease, PMBA ortholog (NCBI ptt file) 91, 225
CAC0290 CAC0290 Sensory transduction histidine kinases (NCBI ptt file) 82, 91
CAC0294 CAC0294 Magnesium and cobalt transporter (NCBI ptt file) 3, 5
CAC0400 CAC0400 Hypothetical protein, CF-19 family (NCBI ptt file) 91, 346
CAC0602 ftsH ATP-dependent zinc metallopeptidase FtsH (cell dividion protein) (NCBI ptt file) 91, 222
CAC0603 CAC0603 Superfamily I DNA and RNA helicase (NCBI ptt file) 91, 225
CAC0764 CAC0764 NADPH-dependent glutamate synthase beta chain (NCBI ptt file) 44, 91
CAC1195 ligA DNA ligase (NAD dependent), LigA (NCBI ptt file) 3, 5
CAC1241 radc RadC protein ortholog (NCBI ptt file) 3, 251
CAC1279 hemN Coproporphyrinogen III oxidase (NCBI ptt file) 3, 106
CAC1309 CAC1309 Hypothetical protein (NCBI ptt file) 3, 51
CAC1540 CAC1540 Uncharacterized ATP-grasp enzyme (NCBI ptt file) 71, 91
CAC1544 CAC1544 Cytidine deaminase, cdd (NCBI ptt file) 91, 225
CAC1546 deoA Pyrimidine-nucleoside phosphorylase (NCBI ptt file) 91, 200
CAC1716 CAC1716 Uncharacterized stress-induced protein, YicC family (NCBI ptt file) 3, 251
CAC1717 CAC1717 Uncharacterized conserved protein, YLOA ortholog (NCBI ptt file) 3, 91
CAC1718 CAC1718 Guanylate kinase, YLOD B.subtilis ortholog (NCBI ptt file) 3, 329
CAC1736 recG RecG helicase (NCBI ptt file) 3, 51
CAC1793 lexA P-loop ATPase domain fused to LexA-like protein (NCBI ptt file) 3, 5
CAC1794 CAC1794 Predicted permease (NCBI ptt file) 3, 51
CAC1796 CAC1796 Predicted membrane-associated Zn-dependent protease (NCBI ptt file) 64, 91
CAC1818 CAC1818 Conserved membrane protein, possible 4-hydroxybenzoate octaprenyltranferase (NCBI ptt file) 3, 51
CAC2032 CAC2032 Hypothetical protein (NCBI ptt file) 3, 258
CAC2065 deoB Phosphopentomutase (NCBI ptt file) 51, 91
CAC2066 CAC2066 Integrase/recombinase XerD family (NCBI ptt file) 51, 91
CAC2125 divIB Cell division septal protein divIB/FtsQ (NCBI ptt file) 2, 3
CAC2296 CAC2296 Uncharacterized protein, YigZ family (NCBI ptt file) 3, 91
CAC2297 CAC2297 Transcriptional regulator of MocR family (DNA-binding HTH domain and aminotransferase domain) (NCBI ptt file) 3, 91
CAC2298 CAC2298 Predicted nucleotidyltransferase (NCBI ptt file) 91, 345
CAC2340 mutS1 DNA mismatch repair protein mutS, YSHD B.subtilis ortholog (NCBI ptt file) 51, 91
CAC2346 CAC2346 Glycosyltransferase (NCBI ptt file) 3, 100
CAC2415 CAC2415 Uncharacterized conserved protein (NCBI ptt file) 91, 289
CAC2550 CAC2550 Hypothetical protein (NCBI ptt file) 3, 258
CAC2674 CAC2674 ATP-dependent superfamily I DNA helicase, PCRA (NCBI ptt file) 3, 98
CAC2736 sbcC ATPase involved in DNA repair (NCBI ptt file) 91, 98
CAC2770 CAC2770 Amino acid transporter (NCBI ptt file) 3, 51
CAC3089 CAC3089 Hypothetical protein (NCBI ptt file) 3, 283
CAC3091 CAC3091 Fumarate hydratase, subunit A (N-terminal domain of FumA E.coli) class I (NCBI ptt file) 3, 13
CAC3299 bdhA NADH-dependent butanol dehydrogenase A (BDH I) (NCBI ptt file) 91, 100
CAC3308 CAC3308 Glycosyltransferase fused to TPR-repeat domain (NCBI ptt file) 3, 190
CAC3392 CAC3392 NADH-dependent butanol dehydrogenase (NCBI ptt file) 62, 91
CAC3571 fabZ Hydroxymyristoyl-(acyl carrier protein) dehydratase (NCBI ptt file) 65, 91
CAC3572 accB Biotin carboxyl carrier protein of acetyl-CoA carboxylase (NCBI ptt file) 44, 91
CAC3577 acp Acyl Carrier Protein, ACP (NCBI ptt file) 91, 225
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 CAC2297
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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