Organism : Clostridium acetobutylicum | Module List :
CAC0144 sfsa

Sugar fermentation-stimulation protein (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
DNA-binding protein, stimulates sugar fermentation cog/ cog
sfsA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0144
(Mouseover regulator name to see its description)

CAC0144 is regulated by 26 influences and regulates 54 modules.
Regulators for CAC0144 sfsa (26)
Regulator Module Operator
CAC0144 363 tf
CAC0191 363 tf
CAC0299 363 tf
CAC1226 363 tf
CAC1426 363 tf
CAC1766 363 tf
CAC1946 363 tf
CAC2060 363 tf
CAC2113 363 tf
CAC2306 363 tf
CAC2307 363 tf
CAC3046 363 tf
CAC0144 154 tf
CAC0189 154 tf
CAC0284 154 tf
CAC0426 154 tf
CAC0929 154 tf
CAC1430 154 tf
CAC2113 154 tf
CAC2143 154 tf
CAC2242 154 tf
CAC3200 154 tf
CAC3429 154 tf
CAC3475 154 tf
CAC3647 154 tf
CAC3695 154 tf

Warning: CAC0144 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
6960 2.80e-06 gGagGtG
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6961 1.70e+02 TAtAagTaGgCAAA
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7374 1.80e-01 a.GaGgTg
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7375 2.60e+01 TGGagGGc
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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 CAC0144

CAC0144 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
DNA-binding protein, stimulates sugar fermentation cog/ cog
sfsA tigr/ tigrfam
Module neighborhood information for CAC0144

CAC0144 has total of 46 gene neighbors in modules 154, 363
Gene neighbors (46)
Gene Common Name Description Module membership
CAC0092 CAC0092 Uncharacterized predicted membrane protein, YTWI B.subtilis ortholog (NCBI ptt file) 305, 363
CAC0144 sfsa Sugar fermentation-stimulation protein (NCBI ptt file) 154, 363
CAC0245 CAC0245 ABC transporter ATP-binding protein (NCBI ptt file) 154, 220
CAC0280 CAC0280 Molybdate transport system, permease component (NCBI ptt file) 317, 363
CAC0281 CAC0281 Molybdate-binding periplasmic protein (NCBI ptt file) 363, 366
CAC0296 csfB Zn-finger containing protein, csfB B.subtilis homolog (NCBI ptt file) 64, 154
CAC0297 CAC0297 Lysine decarboxylase (NCBI ptt file) 73, 363
CAC0480 nrdD Oxygen-sensitive ribonucleoside-triphosphate reductase nrdD (NCBI ptt file) 73, 363
CAC0502 uvrB Excinuclease ABC subunit B (helicase subunit of the DNA excision repair complex) (NCBI ptt file) 154, 335
CAC0503 uvrA Excinuclease ABC subunit A (ATP-ase), (uvrA) (NCBI ptt file) 154, 335
CAC0513 CAC0513 Uncharacterized conserved protein, similar to B.subtilis yvcL (NCBI ptt file) 41, 154
CAC0524 CAC0524 Response regulator (CheY-like and HTH domains) (NCBI ptt file) 154, 230
CAC0526 CAC0526 ABC transporter, ATPase component (NCBI ptt file) 154, 230
CAC0527 CAC0527 Predicted permease, domain duplication (NCBI ptt file) 70, 154
CAC0713 eno Enolase (NCBI ptt file) 128, 363
CAC0715 vacB FUSION ribonuclease and ribosomal protein S1 domain (NCBI ptt file) 313, 363
CAC0717 CAC0717 Predicted membrane protein (NCBI ptt file) 154, 230
CAC0748 CAC0748 Nitroreductase family protein (NCBI ptt file) 154, 255
CAC0749 CAC0749 HD hydrolase superfamily protein (NCBI ptt file) 154, 291
CAC0786 CAC0786 Uncharacterized conserved protein, repeats (NCBI ptt file) 154, 236
CAC0787 CAC0787 Uncharacterized conserved protein, repeats (NCBI ptt file) 73, 154
CAC0845 CAC0845 Ferritin-like protein Rsg (NCBI ptt file) 65, 363
CAC0905 CAC0905 Uncharacterized NAD(FAD)-dependent dehydrogenase (NCBI ptt file) 65, 154
CAC0906 CAC0906 Alanyl-tRNA synthetase related protein (NCBI ptt file) 113, 154
CAC1004 CAC1004 Predicted membrane protein (NCBI ptt file) 154, 230
CAC1304 CAC1304 Uncharacterized conserved protein, predicted metal-binding (NCBI ptt file) 113, 363
CAC1324 CAC1324 Uncharacterized predected metal-binding protein (NCBI ptt file) 204, 363
CAC1426 CAC1426 Possible transcriptional regulator from leucine-rich protein (LRPR) family (NCBI ptt file) 47, 363
CAC1979 CAC1979 Predicted membrane protein (NCBI ptt file) 113, 363
CAC2233 CAC2233 TRNA 5-methylaminomethyl-2-thiouridylate)-methyltransferase, PP-loop ATPase (NCBI ptt file) 329, 363
CAC2543 etfA Electron-transferring flavoprotein large subunit (NCBI ptt file) 41, 363
CAC2607 CAC2607 Short-chain alcohol dehydrogenase family protein (NCBI ptt file) 154, 230
CAC2737 sbcD DNA repair exonuclease (NCBI ptt file) 154, 230
CAC2763 CAC2763 Membrane assosiated methyl-accepting chemotaxis protein with HAMP domain (NCBI ptt file) 154, 230
CAC2824 CAC2824 N-terminal HKD family nuclease fused to DNA/RNA helicases of superfamily II,conserved in Streptomyces (NCBI ptt file) 154, 247
CAC2825 CAC2825 Uncharacterized conserved protein, YQXD B.subtilis ortholog (NCBI ptt file) 154, 230
CAC2921 thiH Thiamine biosynthesis enzyme, thiH (NCBI ptt file) 208, 363
CAC2923 CAC2923 Dinucleotide-utilizing enzyme involved in molybdopterin/thiamine biosynthesis (NCBI ptt file) 208, 363
CAC2945 CAC2945 Possible phosphoglycerate dehydrogenase (NCBI ptt file) 279, 363
CAC2946 CAC2946 Hypothetical protein (NCBI ptt file) 345, 363
CAC2947 topB Topoisomerase B (NCBI ptt file) 65, 154
CAC2977 gatA Glutamyl-tRNAGln amidotransferase subunit A (NCBI ptt file) 221, 363
CAC3302 gerKC Spore germination protein GerKC, membrane protein (NCBI ptt file) 154, 230
CAC3330 CAC3330 Cytochrome P450 family protein, YBDT B.subtilis ortholog (NCBI ptt file) 154, 300
CAC3648 CAC3648 Acetyltransferase (with duplicated domains), possibly RIMI-like protein (NCBI ptt file) 73, 363
CAC3652 alsS Acetolactate synthase (NCBI ptt file) 47, 363
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 CAC0144
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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