Organism : Clostridium acetobutylicum | Module List :
CAC1465

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 CAC1465
(Mouseover regulator name to see its description)

CAC1465 is regulated by 11 influences and regulates 6 modules.
Regulators for CAC1465 (11)
Regulator Module Operator
CAC0183 137 tf
CAC0549 137 tf
CAC1465 137 tf
CAC1675 137 tf
CAC1766 137 tf
CAC1965 137 tf
CAC2842 137 tf
CAC3199 137 tf
CAC3579 137 tf
CAC3603 137 tf
CAC3669 137 tf

Warning: CAC1465 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
6926 5.30e+00 AAGggGca
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6927 5.90e+03 GGaGCG
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7278 2.10e-03 GAGGtgA
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7279 4.40e+03 AGGTGC
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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 CAC1465

CAC1465 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 CAC1465

CAC1465 has total of 33 gene neighbors in modules 137, 313
Gene neighbors (33)
Gene Common Name Description Module membership
CAC0080 agrC Histidine kinase-like ATPase (NCBI ptt file) 137, 241
CAC0252 CAC0252 Molybdate-binding protein (NCBI ptt file) 137, 148
CAC0275 CAC0275 Hypothetical protein (NCBI ptt file) 244, 313
CAC0317 CAC0317 Sensory transduction histidine kinase (NCBI ptt file) 137, 253
CAC0336 CAC0336 Hypothetical protein, CF-22 family (NCBI ptt file) 137, 163
CAC0485 CAC0485 TRNA-processing ribonuclease BN (NCBI ptt file) 137, 258
CAC0703 CAC0703 Sugar ABC-transporter, ATP-ase component (NCBI ptt file) 95, 137
CAC0715 vacB FUSION ribonuclease and ribosomal protein S1 domain (NCBI ptt file) 313, 363
CAC0753 CAC0753 PolyA polymerase related protein (HD hydrolase) and P-loop ATP-ase domain (NCBI ptt file) 137, 353
CAC0839 potB ABC-type spermidine/putrescine transport system, permease component I (NCBI ptt file) 137, 153
CAC1125 CAC1125 Hypothetical protein (NCBI ptt file) 137, 165
CAC1194 CAC1194 Hypothetical protein (NCBI ptt file) 137, 253
CAC1237 CAC1237 Hypothetical protein (NCBI ptt file) 86, 313
CAC1284 prmA SAM-dependent methyltransferase (NCBI ptt file) 47, 137
CAC1352 CAC1352 Membrane associated chemotaxis sensory transducer protein (MSP domain and HAMP domain) (NCBI ptt file) 137, 256
CAC1465 CAC1465 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 137, 313
CAC1476 CAC1476 Proline/glycine betaine ABC-type transport system, permease component (NCBI ptt file) 313, 328
CAC1496 CAC1496 Uncharacterized protein, homolog of YCGL B.subtilis (NCBI ptt file) 71, 137
CAC1607 CAC1607 Hypothetical protein (NCBI ptt file) 4, 137
CAC1631 CAC1631 Biotin synthase family enzyme (NCBI ptt file) 137, 241
CAC1845 motB Flagellar motor protein MotB (NCBI ptt file) 123, 137
CAC2054 CAC2054 Hypothetical protein (NCBI ptt file) 270, 313
CAC2344 CAC2344 LPS biosynthesis protein , RfbU family (NCBI ptt file) 137, 159
CAC2350 CAC2350 Sugar transaminase, involved in dTDP-4-amino-4,6-dideoxyglucose biosynthesis (NCBI ptt file) 100, 137
CAC2400 CAC2400 Serine/threonine kinase related protein, inactivated (HRDL motif absent) (fragment) (NCBI ptt file) 69, 137
CAC2690 CAC2690 Transcriptional regulator, LysR family (NCBI ptt file) 86, 137
CAC2874 CAC2874 UDP-N-acetylglucosamine 2-epimerase (NCBI ptt file) 137, 315
CAC2893 CAC2893 Hypothetical protein (NCBI ptt file) 63, 137
CAC2978 gatC Glu-tRNA amidotransferase, subunit C (NCBI ptt file) 47, 137
CAC3257 CAC3257 Predicted membrane protein (NCBI ptt file) 137, 333
CAC3485 CAC3485 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 206, 313
CAC3493 CAC3493 Predicted transcriptional regulator component, YOBU B.subtilis homolog (NCBI ptt file) 137, 241
CAC3669 CAC3669 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 65, 137
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 CAC1465
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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