Organism : Clostridium acetobutylicum | Module List :
CAC0019

Transcriptional regulator, AcrR family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0019
(Mouseover regulator name to see its description)

CAC0019 is regulated by 17 influences and regulates 7 modules.
Regulators for CAC0019 (17)
Regulator Module Operator
CAC0019 341 tf
CAC1569 341 tf
CAC2394 341 tf
CAC2476 341 tf
CAC2616 341 tf
CAC3647 341 tf
CAC3695 341 tf
CAC0189 73 tf
CAC0195 73 tf
CAC0681 73 tf
CAC1430 73 tf
CAC1509 73 tf
CAC1843 73 tf
CAC2306 73 tf
CAC2608 73 tf
CAC3418 73 tf
CAC3496 73 tf

Warning: CAC0019 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
6800 4.60e-04 GgAGGgg
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6801 6.10e+01 cAtaGGGaG
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7334 8.10e-05 aGGAGG
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7335 7.20e+03 GGGCaaGGTc
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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 CAC0019

CAC0019 is enriched for 5 functions in 3 categories.
Module neighborhood information for CAC0019

CAC0019 has total of 50 gene neighbors in modules 73, 341
Gene neighbors (50)
Gene Common Name Description Module membership
CAC0019 CAC0019 Transcriptional regulator, AcrR family (NCBI ptt file) 73, 341
CAC0130 CAC0130 Uncharacterized membrane protein, YTAF B.subtilis ortholog (NCBI ptt file) 176, 341
CAC0142 CAC0142 Hypothetical protein (NCBI ptt file) 188, 341
CAC0297 CAC0297 Lysine decarboxylase (NCBI ptt file) 73, 363
CAC0480 nrdD Oxygen-sensitive ribonucleoside-triphosphate reductase nrdD (NCBI ptt file) 73, 363
CAC0486 CAC0486 Hypothetical protein (NCBI ptt file) 73, 367
CAC0523 CAC0523 SAM-dependent methyltransferase related to tRNA(uracyl-5-)-methyltransferase (trmA family) (NCBI ptt file) 254, 341
CAC0525 CAC0525 Sensory transduction histidine kinase (HisKA and HATPase_c domains) (NCBI ptt file) 70, 73
CAC0642 CAC0642 Conserved domain seen in the bacterial SpoT (NCBI ptt file) 73, 367
CAC0686 CAC0686 Spore cortex-lytic enzyme prepeptide; peptodoglycan-binding domain (NCBI ptt file) 118, 341
CAC0787 CAC0787 Uncharacterized conserved protein, repeats (NCBI ptt file) 73, 154
CAC0844 CAC0844 Barstar-like protein ribonuclease (barnase) inhibitor (NCBI ptt file) 67, 341
CAC0992 CAC0992 Hypothetical protein (NCBI ptt file) 73, 281
CAC1034 CAC1034 Hypothetical protein (NCBI ptt file) 73, 294
CAC1354 CAC1354 Phosphotransferase system IIA component (NCBI ptt file) 254, 341
CAC1388 manC Mannose-6-phosphate isomerase (NCBI ptt file) 162, 341
CAC1606 CAC1606 Uncharacterized conserved protein (NCBI ptt file) 4, 73
CAC1653 CAC1653 Predicted glycosyltransferases involved in cell wall biogenesis (NCBI ptt file) 73, 118
CAC1658 CAC1658 Phospholipase D family protein (NCBI ptt file) 73, 326
CAC1663 CAC1663 Hypothetical protein (NCBI ptt file) 73, 366
CAC1771 CAC1771 Uncharacterized protein, ykrI B.subtilis homolog (NCBI ptt file) 73, 158
CAC1817 CAC1817 Stage V sporulation protein, spoVS (NCBI ptt file) 38, 73
CAC1831 CAC1831 Protein containing Zn-finger domain (NCBI ptt file) 29, 73
CAC1841 CAC1841 Uncharacterized protein, related to Spore coat protein CotS (NCBI ptt file) 73, 269
CAC2287 CAC2287 Acyl-CoA reductase LuxC (NCBI ptt file) 73, 345
CAC2451 CAC2451 SoxR family transcriptional regulator fused to SAM-dependent methyltransferase (NCBI ptt file) 162, 341
CAC2465 CAC2465 Uncharacterized conserved protein (NCBI ptt file) 73, 367
CAC2480 CAC2480 Predicted acetyltransferase (NCBI ptt file) 73, 228
CAC2502 CAC2502 Predicted permease (NCBI ptt file) 130, 341
CAC2515 CAC2515 Hypothetical protein (NCBI ptt file) 149, 341
CAC2602 CAC2602 Spermidine synthase (NCBI ptt file) 110, 341
CAC2789 CAC2789 Hypothetical protein (NCBI ptt file) 73, 289
CAC2802 CAC2802 Predicted phosphoglycerol transferase (alkaline phosphatase superfamily), YFNI B.subtilis (NCBI ptt file) 73, 367
CAC2823 CAC2823 Hypothetical protein (NCBI ptt file) 258, 341
CAC2919 CAC2919 Hypothetical protein (NCBI ptt file) 24, 73
CAC2982 CAC2982 MinD family ATPase (chromosome partitioning) (NCBI ptt file) 254, 341
CAC3005 add Adenosine deaminase (NCBI ptt file) 40, 341
CAC3019 CAC3019 Sensory transduction protein with GGDEF and EAL domains (NCBI ptt file) 73, 367
CAC3175 CAC3175 Hypothetical protein (NCBI ptt file) 73, 292
CAC3226 CAC3226 Predicted membrane protein (NCBI ptt file) 86, 341
CAC3256 CAC3256 Predicted acetyltransferase (NCBI ptt file) 123, 341
CAC3264 CAC3264 Uncharacterized conserved protein, YTFJ B.subtilis ortholog (NCBI ptt file) 4, 341
CAC3313 CAC3313 Acyl carrier protein, ACP (NCBI ptt file) 86, 341
CAC3341 CAC3341 Multimeric flavodoxin WrbA family protein (NCBI ptt file) 4, 341
CAC3427 CAC3427 PTS system, (possibly glucose-specific) IIA component (NCBI ptt file) 73, 366
CAC3450 CAC3450 Hypothetical protein (NCBI ptt file) 119, 341
CAC3491 CAC3491 Protein, related to general stress protein 26(GS26) of B.subtilis (pyridoxinephosphate oxidase family) (NCBI ptt file) 312, 341
CAC3496 CAC3496 Predicted transcriptional regulator (NCBI ptt file) 179, 341
CAC3648 CAC3648 Acetyltransferase (with duplicated domains), possibly RIMI-like protein (NCBI ptt file) 73, 363
CAC3654 CAC3654 Heavy-metal binding protein (similar to N-terminal domain of MerA) (NCBI ptt file) 73, 320
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 CAC0019
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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