Organism : Clostridium acetobutylicum | Module List :
CAC1511

FNR-like catabolite gene activator (c-AMP binding domain) (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases 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 CAC1511
(Mouseover regulator name to see its description)

CAC1511 is regulated by 21 influences and regulates 2 modules.
Regulators for CAC1511 (21)
Regulator Module Operator
CAC0189 38 tf
CAC0393 38 tf
CAC0559 38 tf
CAC0832 38 tf
CAC1511 38 tf
CAC1695 38 tf
CAC1869 38 tf
CAC2476 38 tf
CAC2616 38 tf
CAC2842 38 tf
CAC0144 240 tf
CAC0191 240 tf
CAC0493 240 tf
CAC0951 240 tf
CAC2236 240 tf
CAC2568 240 tf
CAC3361 240 tf
CAC3370 240 tf
CAC3429 240 tf
CAC3433 240 tf
CAC3472 240 tf

Warning: CAC1511 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
6730 1.90e+00 ataGggGtgA
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6731 1.80e+04 GTAACaGGCtC
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7132 1.80e-03 AAAGGaGg
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7133 3.30e+03 CCCCCTc
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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 CAC1511

CAC1511 is enriched for 4 functions in 3 categories.
Module neighborhood information for CAC1511

CAC1511 has total of 47 gene neighbors in modules 38, 240
Gene neighbors (47)
Gene Common Name Description Module membership
CAC0024 CAC0024 Membrane protein, related to Actinobacillus protein (1944168) (NCBI ptt file) 38, 295
CAC0361 kduD 2 deoxy-D-gluconate 3-dehydrogenase (NCBI ptt file) 65, 240
CAC0720 CAC0720 Hypothetical protein (NCBI ptt file) 223, 240
CAC0762 CAC0762 Permease, probably tetracycline resistance protein (NCBI ptt file) 169, 240
CAC0831 CAC0831 Sensory transduction histidine kinase (NCBI ptt file) 38, 53
CAC0832 CAC0832 Fusion: transcriptional regulator and conserved domain (NCBI ptt file) 38, 320
CAC0842 CAC0842 Hypothetical protein, CF-28 family (NCBI ptt file) 38, 56
CAC0923 CAC0923 Predicted membrane protein; CF_1 family (NCBI ptt file) 148, 240
CAC0947 CAC0947 Predicted membrane protein, hemolysin III homolog (NCBI ptt file) 38, 273
CAC0987 CAC0987 Hypothetical protein (NCBI ptt file) 38, 134
CAC1055 CAC1055 Hypothetical protein (NCBI ptt file) 38, 367
CAC1057 CAC1057 Uncharcterized protein, shares conserved domain among different RHS family proteins and WAPA of B.subtilis (NCBI ptt file) 224, 240
CAC1100 CAC1100 Secreted protein, similar to catalytic domain of murein transglycosylase (NCBI ptt file) 38, 56
CAC1497 CAC1497 Uncharacterized protein, homolog of YCGL B.subtilis (NCBI ptt file) 216, 240
CAC1511 CAC1511 FNR-like catabolite gene activator (c-AMP binding domain) (NCBI ptt file) 38, 240
CAC1512 nirC Formate/nitrite family of transporter (NCBI ptt file) 240, 320
CAC1513 asrA Anaerobic sulfite reductase (Fe-S subunit) (NCBI ptt file) 208, 240
CAC1515 asrC Anaerobic sulfite reduction protein C, reductase (NCBI ptt file) 111, 240
CAC1648 CAC1648 Hypothetical protein, CF-7 family (NCBI ptt file) 206, 240
CAC1688 CAC1688 Penicillin-binding protein (NCBI ptt file) 38, 316
CAC1732 CAC1732 Hypothetical protein (NCBI ptt file) 38, 105
CAC1817 CAC1817 Stage V sporulation protein, spoVS (NCBI ptt file) 38, 73
CAC1819 aspB Aspartate Aminotransferase (NCBI ptt file) 38, 87
CAC2034 CAC2034 Hypothetical protein (NCBI ptt file) 38, 279
CAC2261 CAC2261 HD-hydrolase domain containing protein, YHAM B.subtilis ortholog (NCBI ptt file) 38, 278
CAC2270 CAC2270 Hypothetical protein (NCBI ptt file) 38, 352
CAC2455 CAC2455 Hypothetical protein, CF-13 family (NCBI ptt file) 202, 240
CAC2470 CAC2470 Uncharacterized Zn-finger protein (NCBI ptt file) 38, 78
CAC2476 CAC2476 Uncharacterized protein, homolog of Spirochaeta aurantia (gi:152901) (NCBI ptt file) 38, 304
CAC2477 CAC2477 Hypothetical protein (NCBI ptt file) 38, 304
CAC2539 CAC2539 Predicted acetyltransferase (NCBI ptt file) 240, 265
CAC2589 CAC2589 Glycosyltransferase (NCBI ptt file) 169, 240
CAC2592 CAC2592 6-pyruvoyl-tetrahydropterin synthase related domain; conserved membrane protein (NCBI ptt file) 24, 240
CAC2721 CAC2721 Response regulator (CheY-like reciever domain and HTH-type DNA-binding domain) (NCBI ptt file) 38, 316
CAC2742 CAC2742 Predicted membrane protein (NCBI ptt file) 206, 240
CAC2743 CAC2743 Predicted permease, YXIO B.subtilis ortholog (NCBI ptt file) 26, 240
CAC2888 rpmE 50S ribosomal protein L31 (NCBI ptt file) 38, 304
CAC3206 CAC3206 Ribosomal protein S1 domain family protein (NCBI ptt file) 38, 295
CAC3261 ada Methylated DNA-protein cysteine methyltransferase (NCBI ptt file) 240, 265
CAC3301 gerKB Spore germination protein GerKB, membrane protein (NCBI ptt file) 24, 240
CAC3361 CAC3361 Transcriptional regulator, LysR family (NCBI ptt file) 150, 240
CAC3368 CAC3368 Predicted permease (NCBI ptt file) 148, 240
CAC3370 CAC3370 Predicted transcriptional regulator (NCBI ptt file) 150, 240
CAC3482 CAC3482 Predicted permease (NCBI ptt file) 240, 338
CAC3503 CAC3503 Nucleoside-diphosphate-sugar epimerase (NCBI ptt file) 83, 240
CAC3508 CAC3508 Predicted aminopeptidase (NCBI ptt file) 240, 356
CAC3663 CAC3663 Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 202, 240
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 CAC1511
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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