Organism : Clostridium acetobutylicum | Module List :
CAC0015 serA

D-3-phosphoglycerate dehydrogenase (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Phosphoglycerate dehydrogenase and related dehydrogenases cog/ cog
phosphoglycerate dehydrogenase activity go/ molecular_function
metabolic process go/ biological_process
NAD binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0015
(Mouseover regulator name to see its description)

CAC0015 is regulated by 24 influences and regulates 0 modules.
Regulators for CAC0015 serA (24)
Regulator Module Operator
CAC0201 193 tf
CAC0426 193 tf
CAC1430 193 tf
CAC1578 193 tf
CAC1945 193 tf
CAC2113 193 tf
CAC2430 193 tf
CAC3429 193 tf
CAC3475 193 tf
CAC3611 193 tf
CAC3695 193 tf
CAC0023 250 tf
CAC0144 250 tf
CAC0310 250 tf
CAC0929 250 tf
CAC1280 250 tf
CAC1569 250 tf
CAC2113 250 tf
CAC2430 250 tf
CAC3409 250 tf
CAC3475 250 tf
CAC3606 250 tf
CAC3677 250 tf
CAC3695 250 tf

Warning: CAC0015 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
7038 8.10e+00 GGggGc
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7039 3.20e+03 GACAaTaCG
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7152 1.40e+01 cCTCtTC
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7153 6.30e+02 CAaaacaAGGgg
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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 CAC0015

CAC0015 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Phosphoglycerate dehydrogenase and related dehydrogenases cog/ cog
phosphoglycerate dehydrogenase activity go/ molecular_function
metabolic process go/ biological_process
NAD binding go/ molecular_function
Module neighborhood information for CAC0015

CAC0015 has total of 20 gene neighbors in modules 193, 250
Gene neighbors (20)
Gene Common Name Description Module membership
CAC0014 CAC0014 Aminotransferase (NCBI ptt file) 250, 305
CAC0015 serA D-3-phosphoglycerate dehydrogenase (NCBI ptt file) 193, 250
CAC0016 CAC0016 Related to HTH domain of SpoOJ/ParA/ParB/repB family, involved in chromosome partitioning (NCBI ptt file) 193, 250
CAC0017 serS Seryl-tRNA synthetase (NCBI ptt file) 193, 250
CAC0273 CAC0273 2-isopropylmalate synthase (NCBI ptt file) 196, 250
CAC1390 purE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase (NCBI ptt file) 193, 250
CAC1391 purC Phosphoribosylaminoimidazolesuccinocarboxamide (SAICAR) synthase (NCBI ptt file) 193, 250
CAC1392 purF Glutamine phosphoribosylpyrophosphate amidotransferase (NCBI ptt file) 193, 249
CAC1393 purM Phosphoribosylaminoimidazol (AIR) synthetase (NCBI ptt file) 193, 250
CAC1394 PurN Folate-dependent phosphoribosylglycinamide formyltransferase (NCBI ptt file) 193, 250
CAC1395 purH AICAR transformylase/IMP cyclohydrolase (NCBI ptt file) 193, 249
CAC2644 carB Carbamoylphosphate synthase large subunit (NCBI ptt file) 110, 250
CAC2645 carA Carbamoylphosphate synthase small subunit (NCBI ptt file) 110, 250
CAC3622 CAC3622 Possible subunit of benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase (NCBI ptt file) 193, 249
CAC3624 CAC3624 6-pyruvoyl-tetrahydropterin synthase (NCBI ptt file) 193, 250
CAC3625 CAC3625 Fe-S oxidoreductase of MoaA family (NCBI ptt file) 193, 249
CAC3626 mtrA GTP cyclohydrolase I (NCBI ptt file) 193, 249
CAC3627 CAC3627 PP-loop superfamily ATPase, confers aluminum resistance (NCBI ptt file) 30, 193
CAC3691 CAC3691 Hypothetical protein (NCBI ptt file) 218, 250
CAC3694 CAC3694 TPR-repeat-containing protein (NCBI ptt file) 196, 250
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 CAC0015
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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