Organism : Clostridium acetobutylicum | Module List :
CAC2394

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 CAC2394
(Mouseover regulator name to see its description)

CAC2394 is regulated by 26 influences and regulates 8 modules.
Regulators for CAC2394 (26)
Regulator Module Operator
CAC0032 40 tf
CAC0144 40 tf
CAC0183 40 tf
CAC0191 40 tf
CAC0265 40 tf
CAC0299 40 tf
CAC0550 40 tf
CAC0766 40 tf
CAC0841 40 tf
CAC1355 40 tf
CAC2053 40 tf
CAC2074 40 tf
CAC2113 40 tf
CAC2394 40 tf
CAC2934 40 tf
CAC3149 40 tf
CAC3192 40 tf
CAC0310 231 tf
CAC0807 231 tf
CAC0876 231 tf
CAC1463 231 tf
CAC1469 231 tf
CAC1668 231 tf
CAC2675 231 tf
CAC2934 231 tf
CAC3553 231 tf

Warning: CAC2394 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
6734 1.40e-01 agGAGG
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6735 1.10e+02 GGaaGG
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7114 1.90e-04 GGAGGtaa
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7115 1.50e+00 gcgGcC.agCC.c.AGGGc
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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 CAC2394

CAC2394 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 CAC2394

CAC2394 has total of 40 gene neighbors in modules 40, 231
Gene neighbors (40)
Gene Common Name Description Module membership
CAC0022 asd Aspartate-semialdehyde dehydrogenase (NCBI ptt file) 176, 231
CAC0068 CAC0068 (FS) similar to ABC transporter (permease), YXDM B.subtilis ortholog (NCBI ptt file) 40, 246
CAC0219 CAC0219 Uracyl DNA glycosilase (NCBI ptt file) 40, 160
CAC0331 CAC0331 Uncharacterized membrane protein, homolog of YPAA B.subtilis (NCBI ptt file) 147, 231
CAC0484 CAC0484 Phosphomannomutase (NCBI ptt file) 40, 246
CAC0516 dnaE DNA polimerase III, alpha chain (dnaE) (NCBI ptt file) 146, 231
CAC0557 CAC0557 Predicted Zn-dependent protease with possible chaperone function (NCBI ptt file) 40, 179
CAC0611 CAC0611 Predicted membrane protein, YohK family (NCBI ptt file) 40, 198
CAC0612 CAC0612 Predicted membrane protein YohJ family (NCBI ptt file) 40, 198
CAC0618 CAC0618 Uncharacterised permease, similar to ABC transporter (permease) (NCBI ptt file) 40, 312
CAC0735 CAC0735 Transmembrane protein, ortholog TM1408 (NCBI ptt file) 231, 267
CAC0807 CAC0807 Cold shock protein (NCBI ptt file) 231, 233
CAC0966 CAC0966 Predicted membrane protein (NCBI ptt file) 40, 302
CAC1047 CAC1047 Ribonucleotide reductase, vitamin B12-dependent (NCBI ptt file) 231, 238
CAC1257 rpl21 Ribosomal protein L21 (NCBI ptt file) 61, 231
CAC1288 rpsU Ribosomal protein S21 (NCBI ptt file) 128, 231
CAC1299 dnaG DNA primase, DNAG (NCBI ptt file) 231, 286
CAC1472 CAC1472 Amino acid permease (NCBI ptt file) 40, 267
CAC1532 CAC1532 Protein containing ChW-repeats (NCBI ptt file) 110, 231
CAC1573 CAC1573 Uncharacterized protein, YJDF B.subtilis ortholog (NCBI ptt file) 90, 231
CAC1746 plsX Fatty acid/phospholipid biosynthesis enzyme (NCBI ptt file) 194, 231
CAC2111 CAC2111 Fibronectin-binding protein (NCBI ptt file) 40, 198
CAC2122 CAC2122 Conserved membrane protein (NCBI ptt file) 67, 231
CAC2245 CAC2245 Stress-induced protein OsmC (NCBI ptt file) 40, 130
CAC2293 CAC2293 Hypothetical secreted protein (NCBI ptt file) 110, 231
CAC2393 CAC2393 Uncharacterized ABC transporter, ATPase component (NCBI ptt file) 231, 267
CAC2394 CAC2394 Transcriptional regulator, LysR family (NCBI ptt file) 40, 231
CAC2395 CAC2395 Predicted phosphatase, YWOA B.subtilis ortholog (NCBI ptt file) 40, 130
CAC2482 CAC2482 Carbonic anhydrase (NCBI ptt file) 218, 231
CAC2675 CAC2675 Uncharcterized protein, YECD B.subtilis homolog (NCBI ptt file) 34, 231
CAC2775 CAC2775 Phosphohydrolase from calcineurin family (NCBI ptt file) 11, 231
CAC2934 CAC2934 Predicted transcriptional regulator (NCBI ptt file) 218, 231
CAC2937 CAC2937 Ketopantoate reductase PanE/ApbA (NCBI ptt file) 231, 302
CAC2971 thiI Thiamine biosynthesis enzyme, THII (NCBI ptt file) 40, 198
CAC2972 nifS Possible cysteine desulphurase from NifS family (NCBI ptt file) 40, 319
CAC3005 add Adenosine deaminase (NCBI ptt file) 40, 341
CAC3046 CAC3046 Transcriptional regulator, LytR family (NCBI ptt file) 90, 231
CAC3285 CAC3285 Predicted amino acid transporter (NCBI ptt file) 40, 302
CAC3329 CAC3329 Putative Mn transporter, NRAMP family (NCBI ptt file) 24, 40
CAC3444 CAC3444 Probable cation efflux pump (multidrug resistance protein) (NCBI ptt file) 40, 218
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 CAC2394
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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