Organism : Clostridium acetobutylicum | Module List :
CAC2962

Transcriptional regulators of the LacI family (NCBI ptt file)

CircVis
Functional Annotations (5)
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
alanine racemase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2962
(Mouseover regulator name to see its description)

CAC2962 is regulated by 18 influences and regulates 6 modules.
Regulators for CAC2962 (18)
Regulator Module Operator
CAC0113 346 tf
CAC0174 346 tf
CAC0723 346 tf
CAC0859 346 tf
CAC1766 346 tf
CAC3406 346 tf
CAC3611 346 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: CAC2962 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
7174 1.30e-10 aGGaGG
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7175 6.20e+03 TCcCcTTTCaT
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7344 1.10e-04 AtGGaGG
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7345 6.00e+02 CaGac.ctg.tTaacataa.AagC
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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 CAC2962

CAC2962 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
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
alanine racemase activity go/ molecular_function
Module neighborhood information for CAC2962

CAC2962 has total of 47 gene neighbors in modules 261, 346
Gene neighbors (47)
Gene Common Name Description Module membership
CAC0113 CAC0113 Transcriptional regulator of sugar metabolism (NCBI ptt file) 20, 346
CAC0220 CAC0220 Hypothetical protein (NCBI ptt file) 49, 261
CAC0235 CAC0235 Chloramphenicol acetyltransferase (NCBI ptt file) 140, 346
CAC0236 CAC0236 ABC-type multidrug transport system, ATP-ase component (NCBI ptt file) 140, 346
CAC0238 CAC0238 ABC transporter, permease component (NCBI ptt file) 259, 346
CAC0239 CAC0239 Histidine kinase-like ATPase (NCBI ptt file) 185, 346
CAC0400 CAC0400 Hypothetical protein, CF-19 family (NCBI ptt file) 91, 346
CAC0418 CAC0418 Predicted phosphatase, HAD family (NCBI ptt file) 261, 287
CAC0547 CAC0547 Lactoylglutation lyase (NCBI ptt file) 346, 366
CAC0549 CAC0549 Predicted transcriptional regulator (NCBI ptt file) 74, 261
CAC0648 CAC0648 Molecular chaperone, DnaJ family (contain C-term. Zn finger domain) (NCBI ptt file) 149, 346
CAC0825 CAC0825 Endoglucanase family 5 (NCBI ptt file) 225, 261
CAC0871 CAC0871 Hypothetical protein (NCBI ptt file) 157, 261
CAC0968 CAC0968 Hypothetical protein (NCBI ptt file) 140, 346
CAC1037 CAC1037 Predicted xylanase/chitin deacetylase (NCBI ptt file) 206, 261
CAC1040 CAC1040 Predicted amidohydrolases (NCBI ptt file) 185, 346
CAC1076 CAC1076 Hypothetical protein, CF-32 family (NCBI ptt file) 140, 346
CAC1340 araR Transcriptional regulator of the LacI family (NCBI ptt file) 259, 261
CAC1419 CAC1419 Uncharacterized proteins, homologs of microcin C7 resistance protein MccF (NCBI ptt file) 283, 346
CAC1436 CAC1436 Hypothetical protein (NCBI ptt file) 261, 348
CAC1482 CAC1482 Uncharacterized membrane protein,ortholog of YDFK B.subtilis (NCBI ptt file) 158, 346
CAC1494 CAC1494 Hypothetical protein, CF-32 family (NCBI ptt file) 157, 261
CAC1502 CAC1502 Hypothetical protein (NCBI ptt file) 71, 346
CAC1507 phoR Sensory transduction histidine kinase (with HAMP domain) (NCBI ptt file) 205, 346
CAC1558 CAC1558 ABC-type transport system,membrane ATPase component (NCBI ptt file) 1, 346
CAC1621 CAC1621 Predicted Fe-S oxidoreductase (NCBI ptt file) 71, 261
CAC1622 CAC1622 Pyridoxal kinase related protein (NCBI ptt file) 64, 261
CAC1852 CAC1852 Magnesium and cobalt transport protein (NCBI ptt file) 106, 346
CAC1948 CAC1948 Hypothetical protein (NCBI ptt file) 117, 261
CAC1949 CAC1949 Possible TPR-repeat contaning protein (NCBI ptt file) 117, 261
CAC2174 CAC2174 Glycosyltransferase (NCBI ptt file) 82, 346
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
CAC2453 CAC2453 CBS domain containing protein (NCBI ptt file) 13, 346
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
CAC2554 CAC2554 Hypothetical protein (NCBI ptt file) 13, 346
CAC2661 ftsX Cell division protein FtsX (NCBI ptt file) 72, 346
CAC2696 CAC2696 Predicted membrane protein (NCBI ptt file) 117, 346
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
CAC3279 CAC3279 Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file) 209, 261
CAC3364 CAC3364 Barstar-like protein, ribonuclease (barnase) inhibitor (NCBI ptt file) 92, 346
CAC3387 CAC3387 Pectate lyase (NCBI ptt file) 83, 261
CAC3516 CAC3516 Membrane-associated histidine kinase with HAMP domain (NCBI ptt file) 261, 326
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 CAC2962
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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