Organism : Clostridium acetobutylicum | Module List :
CAC1070

Transcriptional regulator, AcrR family (NCBI ptt file)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1070
(Mouseover regulator name to see its description)

CAC1070 is regulated by 19 influences and regulates 6 modules.
Regulators for CAC1070 (19)
Regulator Module Operator
CAC0032 282 tf
CAC0081 282 tf
CAC0360 282 tf
CAC1070 282 tf
CAC1766 282 tf
CAC2074 282 tf
CAC2546 282 tf
CAC3406 282 tf
CAC3475 282 tf
CAC3512 282 tf
CAC3649 282 tf
CAC0197 183 tf
CAC0723 183 tf
CAC0724 183 tf
CAC1070 183 tf
CAC1766 183 tf
CAC3046 183 tf
CAC3214 183 tf
CAC3487 183 tf

Warning: CAC1070 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
7018 4.90e+04 GGAcGA
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7019 2.00e+00 AaAGgAga
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7216 2.20e-02 AgGAGaG
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7217 1.10e+04 GCAGtaGAACAcC
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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 CAC1070

Warning: No Functional annotations were found!

Module neighborhood information for CAC1070

CAC1070 has total of 47 gene neighbors in modules 183, 282
Gene neighbors (47)
Gene Common Name Description Module membership
CAC0036 CAC0036 Predicted membrane protein, containing FHA domain (NCBI ptt file) 102, 183
CAC0050 CAC0050 Hypothetical protein, CF-3 family K28 (NCBI ptt file) 183, 246
CAC0186 CAC0186 Xre family DNA-binding domain and TPR-repeat-containing protein (NCBI ptt file) 68, 183
CAC0366 CAC0366 Predicted permease (NCBI ptt file) 113, 282
CAC0374 CAC0374 Similar to ABC transporter (permease) (NCBI ptt file) 85, 282
CAC0379 CAC0379 Transcriptional regulator, GntR family (NCBI ptt file) 282, 286
CAC0508 uvrC Excinuclease ABC subunit C (NCBI ptt file) 35, 282
CAC0522 CAC0522 Predicted hydrolase of the HAD superfamily (NCBI ptt file) 66, 282
CAC0576 CAC0576 Hypothetical protein (NCBI ptt file) 115, 183
CAC0640 CAC0640 Predicted phoshohydrolase (NCBI ptt file) 282, 298
CAC0676 pssA Phosphatidylserine synthase (NCBI ptt file) 149, 282
CAC0799 psd Phosphatidylserine decarboxylase (NCBI ptt file) 183, 236
CAC0800 ubiA 4-hydroxybenzoate octaprenyltranferase related protein (NCBI ptt file) 183, 267
CAC0818 CAC0818 Diguanylate cyclase/phosphodiesterase domain (GGDEF) containing protein (NCBI ptt file) 183, 202
CAC1011 CAC1011 Uncharacterized small membrane protein, homolog of ykvA B.subtilis (NCBI ptt file) 282, 309
CAC1061 CAC1061 Uncharcterized protein, shares conserved domain among different RHS family proteins and WAPA of B.subtilis (NCBI ptt file) 183, 253
CAC1070 CAC1070 Transcriptional regulator, AcrR family (NCBI ptt file) 183, 282
CAC1407 CAC1407 PTS system, beta-glucosides-specific IIABC component (NCBI ptt file) 282, 359
CAC1527 CAC1527 Spore germination protein GerKB (NCBI ptt file) 26, 183
CAC1589 malS Malic enzyme (NCBI ptt file) 92, 183
CAC1593 CAC1593 Zn-binding lipoprotein related (surface adhesin A), ADHS (NCBI ptt file) 69, 282
CAC1659 CAC1659 Predicted membrane protein (NCBI ptt file) 270, 282
CAC1704 CAC1704 Hypothetical protein (NCBI ptt file) 183, 336
CAC1777 CAC1777 Nudix (MutT-like) hydrolase (NCBI ptt file) 282, 306
CAC1779 CAC1779 Hypothetical protein (NCBI ptt file) 183, 282
CAC1781 CAC1781 Predicted nucleotidyltransferase (NCBI ptt file) 282, 306
CAC1791 CAC1791 Undecaprenyl pyrophosphate synthase (NCBI ptt file) 282, 345
CAC1792 cdsA CDP-diglyceride synthetase (NCBI ptt file) 282, 352
CAC1984 CAC1984 Predicted permease (NCBI ptt file) 176, 183
CAC1986 CAC1986 Hypothetical protein (NCBI ptt file) 68, 183
CAC2022 moaB Molybdopterin biosynthesis enzyme, moaB (NCBI ptt file) 209, 282
CAC2025 CAC2025 Hypothetical protein (NCBI ptt file) 209, 282
CAC2100 CAC2100 Hypothetical protein (NCBI ptt file) 54, 282
CAC2104 CAC2104 General secretion pathway protein F (NCBI ptt file) 54, 282
CAC2106 CAC2106 Predicted membrane protein (NCBI ptt file) 54, 282
CAC2170 CAC2170 Predicted membrane protein (NCBI ptt file) 282, 283
CAC2226 CAC2226 Enzyme of ILVE/PABC family (branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase) (NCBI ptt file) 282, 328
CAC2292 CAC2292 Predicted membrane protein (NCBI ptt file) 282, 359
CAC2410 recX Uncharacterized protein recX (NCBI ptt file) 282, 283
CAC2442 CAC2442 Hemin permease (NCBI ptt file) 85, 282
CAC2443 CAC2443 Iron (III) ABC transporter, ATPase component (NCBI ptt file) 183, 282
CAC2444 CAC2444 Predicted metal-binding protein (NCBI ptt file) 85, 282
CAC2559 CAC2559 Hypothetical protein (NCBI ptt file) 183, 351
CAC2753 CAC2753 Possible MDR-type permease, YQJV B.subtilis ortholog (NCBI ptt file) 183, 336
CAC2761 CAC2761 Thiamine biosynthesis lipoprotein ApbE (NCBI ptt file) 150, 183
CAC3526 CAC3526 FMN-binding protein (NCBI ptt file) 66, 183
CAC3573 fabF 3-oxoacyl-(acyl-carrier-protein) synthase I (NCBI ptt file) 68, 183
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 CAC1070
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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