Organism : Clostridium acetobutylicum | Module List :
CAC0299

Protein from nitrogen regulatory protein P-II (GLNB) family, ortholog YAAQ B.subtilis (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0299
(Mouseover regulator name to see its description)

CAC0299 is regulated by 21 influences and regulates 21 modules.
Regulators for CAC0299 (21)
Regulator Module Operator
CAC0183 334 tf
CAC0299 334 tf
CAC0569 334 tf
CAC0681 334 tf
CAC0933 334 tf
CAC2060 334 tf
CAC3192 334 tf
CAC3345 334 tf
CAC3475 334 tf
CAC0144 47 tf
CAC0183 47 tf
CAC0231 47 tf
CAC0299 47 tf
CAC0531 47 tf
CAC1404 47 tf
CAC1426 47 tf
CAC1465 47 tf
CAC1467 47 tf
CAC2254 47 tf
CAC3192 47 tf
CAC3731 47 tf

Warning: CAC0299 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
6748 1.40e-09 AgGaGG
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6749 4.30e+03 GTCaGTCccC
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7320 9.60e-03 TtagGAGG
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7321 3.30e+02 CTCccCCC
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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 CAC0299

CAC0299 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
Module neighborhood information for CAC0299

CAC0299 has total of 38 gene neighbors in modules 47, 334
Gene neighbors (38)
Gene Common Name Description Module membership
CAC0091 ilvC Ketol-acid reductoisomerase (NCBI ptt file) 128, 334
CAC0159 CAC0159 Hypothetical protein (NCBI ptt file) 47, 334
CAC0299 CAC0299 Protein from nitrogen regulatory protein P-II (GLNB) family, ortholog YAAQ B.subtilis (NCBI ptt file) 47, 334
CAC0302 CAC0302 Predicted metal-binding protein of ferredoxin fold (NCBI ptt file) 29, 47
CAC0471 CAC0471 GrpE protein HSP-70 cofactor (NCBI ptt file) 47, 221
CAC0535 CAC0535 Metal-dependent hydrolase of the beta-lactamase superfamily II (NCBI ptt file) 47, 291
CAC0824 CAC0824 Thioredoxin (NCBI ptt file) 305, 334
CAC0882 CAC0882 Predicted membrane protein, hemolysin III homolog (NCBI ptt file) 29, 334
CAC0948 CAC0948 Uncharacterized protein, DegV family (NCBI ptt file) 47, 334
CAC1035 CAC1035 Hypothetical protein (NCBI ptt file) 200, 334
CAC1282 dnaK Molecular chaperone DnaK, HSP70 family (NCBI ptt file) 47, 221
CAC1284 prmA SAM-dependent methyltransferase (NCBI ptt file) 47, 137
CAC1426 CAC1426 Possible transcriptional regulator from leucine-rich protein (LRPR) family (NCBI ptt file) 47, 363
CAC1441 CAC1441 Hypothetical protein (NCBI ptt file) 47, 204
CAC1604 CAC1604 Methylglyoxal synthase (NCBI ptt file) 47, 298
CAC1840 CAC1840 Predicted acetyltransferase domain containing protein (NCBI ptt file) 298, 334
CAC1964 rpsA Ribosomal protein S1 (NCBI ptt file) 41, 47
CAC2484 CAC2484 Predicted membrane, YQJA B.subtilis ortholog (NCBI ptt file) 47, 292
CAC2497 CAC2497 Hypothetical secreted protein (NCBI ptt file) 334, 338
CAC2739 CAC2739 Predicted acetyltransferase (NCBI ptt file) 30, 47
CAC2788 CAC2788 Xaa-Pro aminopeptidase family enzyme (NCBI ptt file) 47, 221
CAC2941 CAC2941 HAD superfamily hydrolase (NCBI ptt file) 47, 279
CAC2942 CAC2942 Uncharacterized conserved protein fron YGAG family, predicted metal-dependent enzyme (NCBI ptt file) 47, 63
CAC2975 CAC2975 Hypothetical protein (NCBI ptt file) 47, 172
CAC2978 gatC Glu-tRNA amidotransferase, subunit C (NCBI ptt file) 47, 137
CAC3169 ilvB Acetolactate synthase large subunit (NCBI ptt file) 305, 334
CAC3170 ilvD Dihydroxy-acid dehydratase (NCBI ptt file) 305, 334
CAC3171 leuB Isopropylmalate dehydrogenase (NCBI ptt file) 305, 334
CAC3172 leuD 3-isopropylmalate dehydratase, small subunit (NCBI ptt file) 305, 334
CAC3173 leuC 3-Isopropylmalate dehydratase, large subunit (NCBI ptt file) 305, 334
CAC3174 leuA 2-isopropylmalate synthase (NCBI ptt file) 305, 334
CAC3190 CAC3190 Arginine kinase related enzyme, YACI B.subtilis ortholog (NCBI ptt file) 47, 221
CAC3191 CAC3191 Uncharacterized conserved protein, containing ClpE-like Zn-zinger domain; YACH B.subtilis ortholog (NCBI ptt file) 47, 221
CAC3192 CAC3192 Transciptional regulator CTSR (NCBI ptt file) 47, 221
CAC3617 CAC3617 Uncharacterized membrane protein, YHAG B.subtilis homolog (NCBI ptt file) 80, 334
CAC3652 alsS Acetolactate synthase (NCBI ptt file) 47, 363
CAC3653 CAC3653 Hypothetical protein (NCBI ptt file) 47, 221
CAC3714 CAC3714 Molecular chaperone (small heat shock protein), HSP18 (NCBI ptt file) 47, 221
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 CAC0299
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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