Organism : Clostridium acetobutylicum | Module List :
CAC3502

Transcriptional regulator, fadR 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 CAC3502
(Mouseover regulator name to see its description)

CAC3502 is regulated by 16 influences and regulates 14 modules.
Regulators for CAC3502 (16)
Regulator Module Operator
CAC0115 57 tf
CAC0514 57 tf
CAC2473 57 tf
CAC2950 57 tf
CAC3247 57 tf
CAC3687 57 tf
CAC0162 206 tf
CAC0856 206 tf
CAC0860 206 tf
CAC1355 206 tf
CAC1588 206 tf
CAC2451 206 tf
CAC2546 206 tf
CAC3338 206 tf
CAC3370 206 tf
CAC3502 206 tf

Warning: CAC3502 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
6768 2.90e-03 GGaGG.
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6769 1.10e+04 cCTCCAG
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7064 5.20e-05 GGAGgt
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7065 1.00e+04 AAATtATGtcaAgG
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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 CAC3502

CAC3502 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 CAC3502

CAC3502 has total of 48 gene neighbors in modules 57, 206
Gene neighbors (48)
Gene Common Name Description Module membership
CAC0006 gyrB DNA gyrase (topoisomerase II) B subunit (NCBI ptt file) 57, 64
CAC0087 CAC0087 Predicted Co/Zn/Cd cation transporter (NCBI ptt file) 182, 206
CAC0225 CAC0225 Sensory transduction histidine kinase (NCBI ptt file) 57, 109
CAC0274 ansB Aspartate ammonia-lyase (aspartase) gene ansB(aspA) (NCBI ptt file) 206, 238
CAC0314 CAC0314 Uncharacterized protein homolog YKRK B. subtilis (NCBI ptt file) 57, 207
CAC0315 CAC0315 Predicted acetyltransferase (NCBI ptt file) 11, 206
CAC0321 CAC0321 Response regulator (CheY-like domain, HTH domain) (NCBI ptt file) 182, 206
CAC0558 CAC0558 Hypothetical protein (NCBI ptt file) 201, 206
CAC0604 CAC0604 Acyl carrier protein phosphodiesterase (NCBI ptt file) 57, 279
CAC0856 CAC0856 Transcriptional regulator, LacI family (probably maltose operon transcriptional repressor) (NCBI ptt file) 72, 206
CAC0860 CAC0860 Two-component response regulator (NCBI ptt file) 185, 206
CAC0875 CAC0875 Predicted permease (NCBI ptt file) 206, 253
CAC0900 CAC0900 Possible Zn-finger containing protein (NCBI ptt file) 72, 206
CAC0920 CAC0920 Protein related to MIFH/DOPD protein family, function in bacteria is unknown (NCBI ptt file) 72, 206
CAC1037 CAC1037 Predicted xylanase/chitin deacetylase (NCBI ptt file) 206, 261
CAC1249 minD Septum site-determining protein MinD, ATPase (NCBI ptt file) 206, 244
CAC1418 CAC1418 Nitroreductase family protein (NCBI ptt file) 57, 272
CAC1554 CAC1554 Heavy-metal-associated domain (N-terminus) and membrane-bounded cytochrome biogenesis cycZ-like domain, possible membrane copper tolerance protein (NCBI ptt file) 176, 206
CAC1648 CAC1648 Hypothetical protein, CF-7 family (NCBI ptt file) 206, 240
CAC1857 CAC1857 Predicted metal-dependent peptidase (NCBI ptt file) 57, 64
CAC1859 CAC1859 Hypothetical protein (NCBI ptt file) 57, 64
CAC1955 CAC1955 Hypothetical protein (NCBI ptt file) 57, 109
CAC1973 CAC1973 Hypothetical secreted protein (NCBI ptt file) 57, 322
CAC2063 dacF D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 57, 64
CAC2141 CAC2141 Hypothetical protein (NCBI ptt file) 57, 273
CAC2310 CAC2310 Methenyl tetrahydrofolate cyclohydrolase (serine cycle enzyme) (NCBI ptt file) 57, 294
CAC2474 def N-formylmethionyl-tRNA deformylase (NCBI ptt file) 57, 272
CAC2742 CAC2742 Predicted membrane protein (NCBI ptt file) 206, 240
CAC2950 lacR Lactose phosphotransferase system repressor lacR (NCBI ptt file) 57, 146
CAC2967 CAC2967 Alpha-acetolactate decarboxylase (NCBI ptt file) 152, 206
CAC2987 CAC2987 Primase-like protein, containing TOPRIM domain, YABF B.subtilis ortholog (NCBI ptt file) 57, 273
CAC2993 CAC2993 Uncharacterized protein, YceG B.subtilis homolog (NCBI ptt file) 146, 206
CAC3022 CAC3022 Alpha/beta superfamily hydrolase (NCBI ptt file) 146, 206
CAC3028 CAC3028 Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file) 31, 206
CAC3072 CAC3072 Mannose-1-phosphate guanylyltransferase (NCBI ptt file) 57, 286
CAC3074 CAC3074 Uncharacterized conserved protein (NCBI ptt file) 72, 206
CAC3354 CAC3354 Probable cation efflux pump (multidrug resistance protein) (NCBI ptt file) 206, 266
CAC3373 CAC3373 Pectin methylesterase (NCBI ptt file) 206, 314
CAC3395 CAC3395 Predicted membrane protein (NCBI ptt file) 57, 86
CAC3396 CAC3396 Nudix (MutT) family hydrolase, C4-type Zn-finger domain containing (NCBI ptt file) 57, 322
CAC3464 CAC3464 Uncharacterized conserved protein (fragment) (NCBI ptt file) 182, 206
CAC3484 CAC3484 Short-chain alcohol dehydrogenase family protein (NCBI ptt file) 206, 216
CAC3485 CAC3485 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 206, 313
CAC3502 CAC3502 Transcriptional regulator, fadR family (NCBI ptt file) 57, 206
CAC3568 accA Acetyl-CoA carboxylase alpha subunit (NCBI ptt file) 32, 206
CAC3597 CAC3597 Rubrerythrin (NCBI ptt file) 4, 57
CAC3598 CAC3598 Rubrerythrin (NCBI ptt file) 4, 57
CAC3599 CAC3599 Hypothetical protein (NCBI ptt file) 4, 206
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 CAC3502
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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