Organism : Clostridium acetobutylicum | Module List :
CAC1451

AraC-type DNA-binding domain-containing protein (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1451
(Mouseover regulator name to see its description)

CAC1451 is regulated by 22 influences and regulates 12 modules.
Regulators for CAC1451 (22)
Regulator Module Operator
CAC0174 140 tf
CAC1451 140 tf
CAC1481 140 tf
CAC2608 140 tf
CAC3349 140 tf
CAC3406 140 tf
CAC3509 140 tf
CAC3611 140 tf
CAC3687 140 tf
CAC0195 80 tf
CAC0681 80 tf
CAC0856 80 tf
CAC1032 80 tf
CAC1264 80 tf
CAC1451 80 tf
CAC2306 80 tf
CAC2608 80 tf
CAC3199 80 tf
CAC3360 80 tf
CAC3418 80 tf
CAC3502 80 tf
CAC3649 80 tf

Warning: CAC1451 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
6814 1.10e+01 cacCtCta.Tc
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6815 3.70e+02 CTCtCCT
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6932 5.80e-04 .CCTCC
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6933 1.30e+02 AaCTtTtATGtTAaaaTaTtcaA
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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 CAC1451

CAC1451 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for CAC1451

CAC1451 has total of 46 gene neighbors in modules 80, 140
Gene neighbors (46)
Gene Common Name Description Module membership
CAC0174 CAC0174 Response regulator, CheY-like receiver domain and HTH DNA-binding domain (NCBI ptt file) 140, 283
CAC0195 CAC0195 Predicted transcriptional regulator (NCBI ptt file) 80, 142
CAC0213 CAC0213 Protein containing LysM motif repeat (NCBI ptt file) 80, 110
CAC0235 CAC0235 Chloramphenicol acetyltransferase (NCBI ptt file) 140, 346
CAC0236 CAC0236 ABC-type multidrug transport system, ATP-ase component (NCBI ptt file) 140, 346
CAC0451 CAC0451 Sensory transduction histidine kinase (HAMP, HisKA, HATPase domains) (NCBI ptt file) 13, 140
CAC0589 birA Biotin-(acetyl-CoA carboxylase)ligase (NCBI ptt file) 13, 140
CAC0675 CAC0675 Hypothetical protein (NCBI ptt file) 80, 196
CAC0857 CAC0857 Glucan phosphorylase (NCBI ptt file) 80, 330
CAC0968 CAC0968 Hypothetical protein (NCBI ptt file) 140, 346
CAC0995 CAC0995 Predicted membrane protein (NCBI ptt file) 80, 345
CAC1005 CAC1005 Uncharacterized protein similar to Cylindrotheca fusiformis plasmid hypothetical protein (GI:99319) (NCBI ptt file) 74, 140
CAC1019 CAC1019 Phospholipase C related protein (NCBI ptt file) 62, 80
CAC1020 CAC1020 Hypothetical protein (NCBI ptt file) 80, 367
CAC1031 feoB FeoB-like GTPase, responsible for iron uptake (NCBI ptt file) 80, 83
CAC1045 CAC1045 Predicted permease (NCBI ptt file) 80, 176
CAC1076 CAC1076 Hypothetical protein, CF-32 family (NCBI ptt file) 140, 346
CAC1451 CAC1451 AraC-type DNA-binding domain-containing protein (NCBI ptt file) 80, 140
CAC1481 CAC1481 Transcriptional regulator, LysR family (NCBI ptt file) 140, 158
CAC1499 CAC1499 A/G-specific DNA glycosylase (NCBI ptt file) 140, 158
CAC1504 CAC1504 MDR-type permease (NCBI ptt file) 140, 158
CAC1506 phoP Response regulator (CheY-like receiver domain and a HTH) (NCBI ptt file) 140, 149
CAC1516 CAC1516 Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) 140, 287
CAC1517 CAC1517 Membrane associated sensory transduction histidine kinase (NCBI ptt file) 140, 351
CAC1643 CAC1643 Hypothetical protein, CF-38 family (NCBI ptt file) 115, 140
CAC1697 CAC1697 Uncharacterized conserved protein, YMXH B.subtilis homolog (NCBI ptt file) 80, 142
CAC2449 CAC2449 Predicted flavoprotein (NCBI ptt file) 11, 80
CAC2450 CAC2450 Desulfoferrodoxin (NCBI ptt file) 80, 225
CAC2635 CAC2635 Hypothetical protein (NCBI ptt file) 80, 278
CAC2755 CAC2755 MDR-type ABC transporter (membrane associated ATPase) (NCBI ptt file) 140, 176
CAC2827 CAC2827 S-adenosylmethionine-dependent methyltransferase (NCBI ptt file) 80, 204
CAC2828 CAC2828 Nudix (MutT) family hydrolase/pyrophosphatase (NCBI ptt file) 80, 204
CAC2928 CAC2928 Predicted membrane protein (NCBI ptt file) 140, 158
CAC3008 CAC3008 CBS domain containing protein (NCBI ptt file) 80, 235
CAC3314 CAC3314 Nitroreductase family protein (NCBI ptt file) 27, 80
CAC3349 CAC3349 Transcriptional regulator, LysR family (NCBI ptt file) 66, 140
CAC3374 CAC3374 Predicted acetyltransferase (NCBI ptt file) 140, 162
CAC3393 CAC3393 Hypothetical protein (NCBI ptt file) 80, 367
CAC3406 CAC3406 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 140, 344
CAC3454 CAC3454 Predicted TIM-barrel enzyme, nifR3 family (NCBI ptt file) 80, 142
CAC3512 CAC3512 AraC-type DNA-binding domain-containing protein (NCBI ptt file) 74, 140
CAC3617 CAC3617 Uncharacterized membrane protein, YHAG B.subtilis homolog (NCBI ptt file) 80, 334
CAC3618 CAC3618 ABC-type polar amino acid transport system, ATPase component (NCBI ptt file) 80, 196
CAC3619 CAC3619 Amino acid ABC transporter, permease component (NCBI ptt file) 80, 196
CAC3620 CAC3620 Amino acid (probably glutamine) ABC transporter, periplasmic binding protein component (NCBI ptt file) 80, 196
CAC3687 CAC3687 Transcriptional regulator, AcrR family (NCBI ptt file) 140, 259
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 CAC1451
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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