Organism : Clostridium acetobutylicum | Module List :
CAC3518

Transcriptional regulators, 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 CAC3518
(Mouseover regulator name to see its description)

CAC3518 is regulated by 21 influences and regulates 10 modules.
Regulators for CAC3518 (21)
Regulator Module Operator
CAC0708 359 tf
CAC0832 359 tf
CAC1578 359 tf
CAC1695 359 tf
CAC1869 359 tf
CAC2254 359 tf
CAC2306 359 tf
CAC3166 359 tf
CAC3247 359 tf
CAC3518 359 tf
CAC0113 225 tf
CAC1264 225 tf
CAC1451 225 tf
CAC2209 225 tf
CAC2608 225 tf
CAC2634 225 tf
CAC2889 225 tf
CAC3152 225 tf
CAC3443 225 tf
CAC3518 225 tf
CAC3611 225 tf

Warning: CAC3518 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
7102 8.80e-08 aaaGGtGatg
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7103 1.00e+03 TgcTttcGcc
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7368 1.10e+03 CCCC.TA
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7369 5.40e+03 CAGGCG
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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 CAC3518

CAC3518 is enriched for 5 functions in 3 categories.
Module neighborhood information for CAC3518

CAC3518 has total of 50 gene neighbors in modules 225, 359
Gene neighbors (50)
Gene Common Name Description Module membership
CAC0229 CAC0229 Predicted Zn-dependent proteases, TLDD ortholog (NCBI ptt file) 91, 225
CAC0230 CAC0230 Inactivated predicted Zn-dependent protease, PMBA ortholog (NCBI ptt file) 91, 225
CAC0270 CAC0270 Hypothetical protein (NCBI ptt file) 67, 225
CAC0433 CAC0433 Methyl-accepting chemotaxis protein (NCBI ptt file) 20, 225
CAC0454 CAC0454 Predicted ATP transporter permease component (NCBI ptt file) 343, 359
CAC0482 CAC0482 Zn-dependent hydrolases of the metallo-beta-lactamase superfamily (NCBI ptt file) 225, 239
CAC0603 CAC0603 Superfamily I DNA and RNA helicase (NCBI ptt file) 91, 225
CAC0700 cspR Predicted tRNA-methylase (SpoU class) (NCBI ptt file) 350, 359
CAC0708 CAC0708 Putative transcriptional regulator (NCBI ptt file) 20, 359
CAC0825 CAC0825 Endoglucanase family 5 (NCBI ptt file) 225, 261
CAC0826 CAC0826 Endoglucanase family 5 (NCBI ptt file) 151, 359
CAC1036 pykA Pyruvate kinase (NCBI ptt file) 348, 359
CAC1152 CAC1152 Hypothetical protein (NCBI ptt file) 16, 359
CAC1407 CAC1407 PTS system, beta-glucosides-specific IIABC component (NCBI ptt file) 282, 359
CAC1544 CAC1544 Cytidine deaminase, cdd (NCBI ptt file) 91, 225
CAC1660 CAC1660 Butyrate kinase, buk (NCBI ptt file) 332, 359
CAC1677 CAC1677 Predicted permease (NCBI ptt file) 259, 359
CAC1909 rnd Ribonuclease D (NCBI ptt file) 225, 277
CAC1910 CAC1910 Predicted membrane protein (NCBI ptt file) 225, 277
CAC2056 CAC2056 Hypothetical protein (NCBI ptt file) 26, 359
CAC2139 flgG Flagellar basal body rod protein (NCBI ptt file) 192, 225
CAC2140 flgG Flagellar basal body rod protein (NCBI ptt file) 192, 359
CAC2215 fliY Flagellar switch protein FliY, contains CheC-like domain (NCBI ptt file) 122, 359
CAC2255 CAC2255 Predicted permease (NCBI ptt file) 336, 359
CAC2292 CAC2292 Predicted membrane protein (NCBI ptt file) 282, 359
CAC2337 CAC2337 Phosphomannomutase (NCBI ptt file) 225, 294
CAC2450 CAC2450 Desulfoferrodoxin (NCBI ptt file) 80, 225
CAC2523 CAC2523 Glycosyltransferase (NCBI ptt file) 191, 359
CAC2601 CAC2601 S-adenosylmethionine decarboxylase (NCBI ptt file) 82, 225
CAC2634 CAC2634 Ferric uptake regulator (FUR family), YGAG B.subtilis ortholog (NCBI ptt file) 49, 225
CAC2655 CAC2655 Uncharacterized membrane-associated protein, DedA family (NCBI ptt file) 26, 359
CAC2725 CAC2725 Predicted hydrolase from alpha/beta family, YQKD B.subtilis ortholog (NCBI ptt file) 51, 225
CAC2732 CAC2732 ABC transporter, ATPase component (NCBI ptt file) 69, 359
CAC2785 CAC2785 Hypothetical protein (NCBI ptt file) 134, 225
CAC2897 CAC2897 Predicted UDP-glucuronosyltransferase, YPFP B/subtilis ortholog (NCBI ptt file) 225, 286
CAC2914 panB Ketopantoate hydroxymethyltransferase (NCBI ptt file) 225, 235
CAC3085 CAC3085 TPR-repeat-containing protein; Cell-adhesion domain (NCBI ptt file) 225, 344
CAC3086 CAC3086 Protein containing cell adhesion domain (NCBI ptt file) 225, 344
CAC3225 murC UDP-N-acetylmuramate-alanine ligase (NCBI ptt file) 292, 359
CAC3247 CAC3247 Predicted transcriptional regulator, lacI/xre family (NCBI ptt file) 151, 359
CAC3248 CAC3248 Hypothetical protein (NCBI ptt file) 157, 225
CAC3249 CAC3249 Hypothetical protein (NCBI ptt file) 157, 225
CAC3251 CAC3251 Sensory transduction protein containing HD_GYP domain (NCBI ptt file) 63, 225
CAC3267 CAC3267 Specialized sigma subunit of RNA polymerase (NCBI ptt file) 99, 225
CAC3272 CAC3272 Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file) 285, 359
CAC3384 CAC3384 Protein chain release factor B (NCBI ptt file) 343, 359
CAC3435 CAC3435 Hypothetical protein (NCBI ptt file) 185, 359
CAC3518 CAC3518 Transcriptional regulators, AcrR family (NCBI ptt file) 225, 359
CAC3570 accC Biotin carboxylase (NCBI ptt file) 44, 225
CAC3577 acp Acyl Carrier Protein, ACP (NCBI ptt file) 91, 225
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 CAC3518
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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