Organism : Clostridium acetobutylicum | Module List :
CAC3649 spoVT

Possible stage V sporulation protein T, transcriptional regulator AbrB homolog (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Regulators of stationary/sporulation gene expression cog/ cog
lp_hng_hel_AbrB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3649
(Mouseover regulator name to see its description)

CAC3649 is regulated by 19 influences and regulates 25 modules.
Regulators for CAC3649 spoVT (19)
Regulator Module Operator
CAC0360 247 tf
CAC0459 247 tf
CAC2242 247 tf
CAC2254 247 tf
CAC3236 247 tf
CAC3349 247 tf
CAC3481 247 tf
CAC3509 247 tf
CAC3525 247 tf
CAC3649 247 tf
CAC0144 108 tf
CAC2605 108 tf
CAC3271 108 tf
CAC3324 108 tf
CAC3429 108 tf
CAC3466 108 tf
CAC3472 108 tf
CAC3649 108 tf
CAC3677 108 tf

Warning: CAC3649 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
6868 1.90e-10 aGGAGg
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6869 6.30e+03 atTGgAGaAgg
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7146 2.30e-04 ttaGGAGg
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7147 4.00e-02 c.G.GgTaCcGcg
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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 CAC3649

CAC3649 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Regulators of stationary/sporulation gene expression cog/ cog
lp_hng_hel_AbrB tigr/ tigrfam
Module neighborhood information for CAC3649

CAC3649 has total of 44 gene neighbors in modules 108, 247
Gene neighbors (44)
Gene Common Name Description Module membership
CAC0071 CAC0071 Uncharacterized conserved protein, YTFE E.coli ortholog (NCBI ptt file) 24, 108
CAC0122 cheY Chemotaxis respons regulator (cheY) (NCBI ptt file) 167, 247
CAC0124 CAC0124 Hypothetical protein (NCBI ptt file) 108, 150
CAC0132 CAC0132 Hypothetical protein (NCBI ptt file) 247, 270
CAC0134 CAC0134 Hypothetical protein, CF-19 family (NCBI ptt file) 62, 247
CAC0135 CAC0135 Hypothetical protein, CF-23 family (NCBI ptt file) 13, 247
CAC0145 CAC0145 N-terminal Zn-ribbon domain and C-terminal MutT domain, YJAD ortholog (NCBI ptt file) 92, 108
CAC0161 CAC0161 ABC transporter (permease) (NCBI ptt file) 108, 144
CAC0295 CAC0295 Metal-dependent amidohydrolases (NCBI ptt file) 108, 190
CAC0419 CAC0419 Predicted membrane protein (NCBI ptt file) 247, 351
CAC0420 CAC0420 Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file) 185, 247
CAC0428 CAC0428 Sugar permease (NCBI ptt file) 108, 145
CAC0477 CAC0477 AP superfamily (NCBI ptt file) 247, 258
CAC0487 CAC0487 Uncharacterized protein, ortholog of Thermotoga maritima (4981823) (NCBI ptt file) 247, 259
CAC0536 dltE Short-chain dehydrodenase (gene dltE) (NCBI ptt file) 71, 108
CAC0626 trpS Tryptophan-tRNA synthetase, trpS (NCBI ptt file) 247, 296
CAC0812 CAC0812 Pectate lyase related protein, secreted (NCBI ptt file) 108, 326
CAC0921 CAC0921 Metal-dependent amidohydrolase (NCBI ptt file) 24, 108
CAC1017 CAC1017 SpoVB related membrane protein (NCBI ptt file) 108, 169
CAC1492 CAC1492 Uncharacterized protein, YhhW/pirin family (NCBI ptt file) 92, 108
CAC1495 CAC1495 Enzyme of dihydrofolate reductase family, ortholog YWFD B.subtilis (NCBI ptt file) 5, 247
CAC2242 CAC2242 Predicted transcriptional regulator, arsE family (NCBI ptt file) 214, 247
CAC2824 CAC2824 N-terminal HKD family nuclease fused to DNA/RNA helicases of superfamily II,conserved in Streptomyces (NCBI ptt file) 154, 247
CAC2902 CAC2902 Isopentenyl monophosphate kinase, IPK (NCBI ptt file) 66, 247
CAC2973 kdgA 2-keto-3-deoxy-6-phosphogluconate aldolase, eda/kdgA (NCBI ptt file) 108, 247
CAC2997 CAC2997 Uracil-DNA glycosylase (NCBI ptt file) 108, 230
CAC3232 CAC3232 Hypothetical protein (NCBI ptt file) 62, 247
CAC3236 CAC3236 Possible transcriptional regulator from YAEG/LRPR family (NCBI ptt file) 247, 312
CAC3270 CAC3270 Permease, predicted cation efflux pump (NCBI ptt file) 108, 145
CAC3380 CAC3380 Metallo-beta-lactamase superfamily hydrolase (NCBI ptt file) 108, 247
CAC3398 CAC3398 Uncharacterized conserved protein, YbhB family (NCBI ptt file) 108, 324
CAC3399 CAC3399 Predicted transcriptional regulator (NCBI ptt file) 108, 324
CAC3474 CAC3474 Predicted MDR-type permease (NCBI ptt file) 108, 356
CAC3481 CAC3481 Transcriptional regulator, AcrR family (NCBI ptt file) 167, 247
CAC3495 CAC3495 Multimeric flavodoxin WrbA family protein (NCBI ptt file) 108, 288
CAC3501 CAC3501 Predicted phosphosugar isomerase (NCBI ptt file) 108, 230
CAC3523 CAC3523 Hypothetical protein, CF-7 family (NCBI ptt file) 108, 226
CAC3524 CAC3524 Hypothetical protein, CF-7 family (NCBI ptt file) 226, 247
CAC3531 CAC3531 IS605/IS200-like transposase (NCBI ptt file) 190, 247
CAC3562 CAC3562 HD superfamily hydrolase (NCBI ptt file) 127, 247
CAC3563 CAC3563 Mismatch repair protein MutS-like ATPase (NCBI ptt file) 247, 335
CAC3649 spoVT Possible stage V sporulation protein T, transcriptional regulator AbrB homolog (NCBI ptt file) 108, 247
CAC3655 CAC3655 Heavy-metal transporting P-type ATPase (NCBI ptt file) 108, 357
CAC3677 kdpE KDP operon transcriptional regulatory protein KdpE (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 108, 247
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 CAC3649
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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