Organism : Clostridium acetobutylicum | Module List :
CAC1340 araR

Transcriptional regulator of the LacI family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1340
(Mouseover regulator name to see its description)

CAC1340 is regulated by 24 influences and regulates 7 modules.
Regulators for CAC1340 araR (24)
Regulator Module Operator
CAC0201 259 tf
CAC0360 259 tf
CAC0821 259 tf
CAC1340 259 tf
CAC2473 259 tf
CAC2605 259 tf
CAC2608 259 tf
CAC2690 259 tf
CAC3142 259 tf
CAC3166 259 tf
CAC3509 259 tf
CAC3611 259 tf
CAC3687 259 tf
CAC0174 261 tf
CAC0549 261 tf
CAC0723 261 tf
CAC1340 261 tf
CAC1451 261 tf
CAC2552 261 tf
CAC2568 261 tf
CAC2962 261 tf
CAC3267 261 tf
CAC3466 261 tf
CAC3579 261 tf

Warning: CAC1340 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
7170 7.20e+03 GaCcGGC
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7171 6.50e+01 aGaAagaGAGg
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7174 1.30e-10 aGGaGG
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7175 6.20e+03 TCcCcTTTCaT
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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 CAC1340

CAC1340 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for CAC1340

CAC1340 has total of 48 gene neighbors in modules 259, 261
Gene neighbors (48)
Gene Common Name Description Module membership
CAC0201 CAC0201 Transcriptional regulators, AcrR family (NCBI ptt file) 157, 259
CAC0220 CAC0220 Hypothetical protein (NCBI ptt file) 49, 261
CAC0238 CAC0238 ABC transporter, permease component (NCBI ptt file) 259, 346
CAC0291 CAC0291 FUSION: methionine sintase I (cobalamin dependent) and 5,10 methylenetetrahydrofolate reductase (NCBI ptt file) 259, 287
CAC0360 CAC0360 Transcriptional regulator, LacI family (HTH lacI domain), B.subtilis degA ortholog (NCBI ptt file) 10, 259
CAC0389 CAC0389 Hypothetical protein (NCBI ptt file) 167, 259
CAC0418 CAC0418 Predicted phosphatase, HAD family (NCBI ptt file) 261, 287
CAC0421 CAC0421 Uncharacterized membrane protein (NCBI ptt file) 72, 259
CAC0487 CAC0487 Uncharacterized protein, ortholog of Thermotoga maritima (4981823) (NCBI ptt file) 247, 259
CAC0549 CAC0549 Predicted transcriptional regulator (NCBI ptt file) 74, 261
CAC0825 CAC0825 Endoglucanase family 5 (NCBI ptt file) 225, 261
CAC0871 CAC0871 Hypothetical protein (NCBI ptt file) 157, 261
CAC1037 CAC1037 Predicted xylanase/chitin deacetylase (NCBI ptt file) 206, 261
CAC1273 CAC1273 Uncharacterized protein, YQEN B.subtilis homolog (NCBI ptt file) 146, 259
CAC1340 araR Transcriptional regulator of the LacI family (NCBI ptt file) 259, 261
CAC1436 CAC1436 Hypothetical protein (NCBI ptt file) 261, 348
CAC1490 CAC1490 Hypothetical protein (NCBI ptt file) 185, 259
CAC1494 CAC1494 Hypothetical protein, CF-32 family (NCBI ptt file) 157, 261
CAC1581 CAC1581 Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) 185, 259
CAC1582 CAC1582 Membrane associated histidine kinase-like ATPase (NCBI ptt file) 259, 287
CAC1619 CAC1619 Hypothetical protein (NCBI ptt file) 71, 259
CAC1621 CAC1621 Predicted Fe-S oxidoreductase (NCBI ptt file) 71, 261
CAC1622 CAC1622 Pyridoxal kinase related protein (NCBI ptt file) 64, 261
CAC1677 CAC1677 Predicted permease (NCBI ptt file) 259, 359
CAC1948 CAC1948 Hypothetical protein (NCBI ptt file) 117, 261
CAC1949 CAC1949 Possible TPR-repeat contaning protein (NCBI ptt file) 117, 261
CAC2364 CAC2364 Uncharacterized protein, homolog of gi|2274936 Eubacterium acidaminophilum (NCBI ptt file) 158, 261
CAC2429 CAC2429 Predicted membrane protein (NCBI ptt file) 259, 261
CAC2472 CAC2472 Alpha/beta superfamily hydrolase (NCBI ptt file) 261, 287
CAC2475 CAC2475 Possible 5-Nitroimidazole antibiotics resistance protein, NimA-family (NCBI ptt file) 261, 276
CAC2496 CAC2496 Predicted phosphatase of HAD hydrolase superfamily (NCBI ptt file) 158, 261
CAC2710 etfB Electron transfer flavoprotein beta-subunit (NCBI ptt file) 255, 259
CAC2778 CAC2778 Rubredoxin (NCBI ptt file) 31, 259
CAC2779 CAC2779 Hypothetical protein (NCBI ptt file) 20, 259
CAC2780 CAC2780 Spore coat protein, cotF related (NCBI ptt file) 20, 259
CAC2832 CAC2832 PLP-dependent aminotransferase (NCBI ptt file) 261, 356
CAC2962 CAC2962 Transcriptional regulators of the LacI family (NCBI ptt file) 261, 346
CAC2986 ksgA Dimethyladenosine transferase (NCBI ptt file) 157, 261
CAC2996 CAC2996 Superfamily II DNA/RNA helicase, SNF2 family (NCBI ptt file) 259, 287
CAC3279 CAC3279 Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file) 209, 261
CAC3387 CAC3387 Pectate lyase (NCBI ptt file) 83, 261
CAC3516 CAC3516 Membrane-associated histidine kinase with HAMP domain (NCBI ptt file) 261, 326
CAC3529 CAC3529 Hypothetical protein (NCBI ptt file) 71, 259
CAC3530 CAC3530 Hypothetical protein (NCBI ptt file) 71, 259
CAC3546 CAC3546 Highly conserved protein containing a domain related to cellulase catalitic domain and a thioredoxin domain (NCBI ptt file) 259, 300
CAC3591 CAC3591 Acyl-ACP thioesterase (NCBI ptt file) 157, 259
CAC3601 CAC3601 Nudix (MutT) family hydrolase (NCBI ptt file) 62, 259
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 CAC1340
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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