Organism : Clostridium acetobutylicum | Module List :
CAC3643

Oligopeptide ABC transporter, permease component (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
transport go/ biological_process
nickel-transporting ATPase activity go/ molecular_function
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3643
(Mouseover regulator name to see its description)

CAC3643 is regulated by 27 influences and regulates 0 modules.
Regulators for CAC3643 (27)
Regulator Module Operator
CAC0032 217 tf
CAC0078 217 tf
CAC0289 217 tf
CAC0360 217 tf
CAC0445 217 tf
CAC0571 217 tf
CAC0821 217 tf
CAC1766 217 tf
CAC2209 217 tf
CAC2306 217 tf
CAC2634 217 tf
CAC3409 217 tf
CAC3429 217 tf
CAC3512 217 tf
CAC3518 217 tf
CAC3729 217 tf
CAC0183 43 tf
CAC0189 43 tf
CAC0310 43 tf
CAC0402 43 tf
CAC0426 43 tf
CAC0474 43 tf
CAC0571 43 tf
CAC0951 43 tf
CAC0977 43 tf
CAC1832 43 tf
CAC2236 43 tf

Warning: CAC3643 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
6740 1.80e-03 GGaGGaA
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6741 1.90e+03 GATGcAacGGAG
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7086 2.10e+00 GgGgGgtg
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7087 3.00e+02 GAaCacgatagCAcC
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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 CAC3643

CAC3643 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
transport go/ biological_process
nickel-transporting ATPase activity go/ molecular_function
membrane go/ cellular_component
Module neighborhood information for CAC3643

CAC3643 has total of 29 gene neighbors in modules 43, 217
Gene neighbors (29)
Gene Common Name Description Module membership
CAC0306 CAC0306 SAM-dependent methyltransferase (NCBI ptt file) 217, 353
CAC0307 CAC0307 Predicted methyltransferase (NCBI ptt file) 191, 217
CAC0395 kdgK 2-keto-3-deoxygluconate kinase (gene kdgK) (NCBI ptt file) 43, 65
CAC0415 CAC0415 TPR-repeat-containing protein (NCBI ptt file) 151, 217
CAC0416 CAC0416 TPR-repeat-containing protein (NCBI ptt file) 151, 217
CAC0424 CAC0424 Fructokinase (NCBI ptt file) 43, 284
CAC0426 CAC0426 Transcriptional regulator (HTH_ARAC-domain) (NCBI ptt file) 43, 343
CAC0532 CAC0532 PTS system, arbutin-like IIBC component (NCBI ptt file) 43, 284
CAC0561 CAC0561 Cellulase CelE ortholog; dockerin domain (NCBI ptt file) 43, 265
CAC0698 CAC0698 Predicted hydrolase of the HAD superfamily (NCBI ptt file) 217, 351
CAC0699 CAC0699 Spore photoproduct lyase, splB (NCBI ptt file) 9, 217
CAC0908 CAC0908 Dinucleotide-utilizing enzyme involved in molybdopterin and thiamine biosynthesis family 1 (NCBI ptt file) 217, 324
CAC1008 CAC1008 Hypothetical protein, CF-30 family (NCBI ptt file) 43, 343
CAC1690 pilT PilT ATPase involved in pili biogenesis (NCBI ptt file) 92, 217
CAC2166 CAC2166 Nucleoside-diphosphate-sugar epimerase (NCBI ptt file) 96, 217
CAC2718 CAC2718 Ethanolamine ammonia lyase large subunit (NCBI ptt file) 43, 111
CAC3177 cysS Cysteinyl-tRNA synthetase (NCBI ptt file) 191, 217
CAC3178 proS Prolyl-tRNA synthetase (NCBI ptt file) 191, 217
CAC3352 CAC3352 Membrane associated methyl-accepting chemotaxis protein with HAMP domain (NCBI ptt file) 151, 217
CAC3492 CAC3492 Uncharacterized conserved protein (NCBI ptt file) 205, 217
CAC3506 CAC3506 Predicted MDR-type permease (NCBI ptt file) 43, 125
CAC3515 CAC3515 Alpha/beta superfamily hydrolase (possible peptidase) (NCBI ptt file) 43, 230
CAC3517 CAC3517 Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 217, 326
CAC3544 CAC3544 Membrane associated GGDEF domain containing protein (NCBI ptt file) 191, 217
CAC3545 CAC3545 Methyl-accepting chemotaxis protein (NCBI ptt file) 191, 217
CAC3642 CAC3642 Oligopeptide ABC transporter, ATPase component (NCBI ptt file) 65, 217
CAC3643 CAC3643 Oligopeptide ABC transporter, permease component (NCBI ptt file) 43, 217
CAC3644 CAC3644 Oligopeptide ABC transporter, permease component (NCBI ptt file) 217, 301
CAC3702 CAC3702 Hypothetical protein, CF-7 family (NCBI ptt file) 43, 343
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 CAC3643
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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