Organism : Clostridium acetobutylicum | Module List :
CAC3201

Formate--tetrahydrofolate ligase (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Formyltetrahydrofolate synthetase cog/ cog
formate-tetrahydrofolate ligase activity go/ molecular_function
ATP binding go/ molecular_function
folic acid-containing compound biosynthetic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3201
(Mouseover regulator name to see its description)

CAC3201 is regulated by 27 influences and regulates 0 modules.
Regulators for CAC3201 (27)
Regulator Module Operator
CAC0019 292 tf
CAC0078 292 tf
CAC0115 292 tf
CAC0474 292 tf
CAC1046 292 tf
CAC1086 292 tf
CAC1588 292 tf
CAC1945 292 tf
CAC1965 292 tf
CAC2071 292 tf
CAC3104 292 tf
CAC3224 292 tf
CAC3418 292 tf
CAC0183 201 tf
CAC0191 201 tf
CAC0493 201 tf
CAC0951 201 tf
CAC1280 201 tf
CAC1559 201 tf
CAC1900 201 tf
CAC2084 201 tf
CAC2690 201 tf
CAC3037 201 tf
CAC3152 201 tf
CAC3651 201 tf
CAC3729 201 tf
CAC3731 201 tf

Warning: CAC3201 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
7054 1.60e-07 aggGGtG
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7055 3.20e+03 GGAGCGaTcAC
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7236 3.10e-03 GGaGgG
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7237 6.90e+03 cGcCACAaGG
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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 CAC3201

CAC3201 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Formyltetrahydrofolate synthetase cog/ cog
formate-tetrahydrofolate ligase activity go/ molecular_function
ATP binding go/ molecular_function
folic acid-containing compound biosynthetic process go/ biological_process
Module neighborhood information for CAC3201

CAC3201 has total of 45 gene neighbors in modules 201, 292
Gene neighbors (45)
Gene Common Name Description Module membership
CAC0082 CAC0082 Predicted membrane protein (NCBI ptt file) 178, 292
CAC0217 pheA Prephenate dehydrotase (pheA) (NCBI ptt file) 182, 292
CAC0272 CAC0272 Amino acid transporter (NCBI ptt file) 201, 215
CAC0330 CAC0330 Propiloprotein diacylglyceryltransferase (NCBI ptt file) 201, 215
CAC0476 pepT Peptidase T (aminotripeptidase), gene pepT (NCBI ptt file) 286, 292
CAC0558 CAC0558 Hypothetical protein (NCBI ptt file) 201, 206
CAC0651 CAC0651 Hypothetical protein (NCBI ptt file) 292, 352
CAC0689 ntH Predicted endonuclease, gene nth (NCBI ptt file) 58, 201
CAC0711 tpi Triosephosphate isomerase (NCBI ptt file) 128, 292
CAC0712 pgm 2,3-bisphosphoglycerate-independent phosphoglycerate mutase gene (NCBI ptt file) 20, 292
CAC0944 tkt Transketolase (NCBI ptt file) 84, 292
CAC0961 CAC0961 Cobyric acid synthase CobQ (NCBI ptt file) 151, 201
CAC0993 dacF D-alanyl-D-alanine carboxypeptidase (penicilin binding protein) (NCBI ptt file) 201, 352
CAC1280 hrcA Transcriptional regulator of heat shock genes, HrcA (NCBI ptt file) 128, 201
CAC1285 CAC1285 Uncharacterized conserved protein, ortholog of YQEU B.subtilis (NCBI ptt file) 201, 352
CAC1356 thiH Thiamine biosynthesis enzyme ThiH (NCBI ptt file) 196, 292
CAC1386 CAC1386 Zn-dependent hydrolases, glyoxylase family (NCBI ptt file) 182, 292
CAC1691 CAC1691 Predicted glycosyltransferase (NCBI ptt file) 201, 211
CAC1692 ftsA Cell division protein, ftsA (NCBI ptt file) 29, 201
CAC1807 rpsO Ribosomal Protein S15 (NCBI ptt file) 201, 352
CAC2120 CAC2120 Uncharacterized protein, YlmF B.subtilis ortholog (NCBI ptt file) 25, 201
CAC2121 CAC2121 Predicted enzyme with a TIM-barrel fold (NCBI ptt file) 11, 201
CAC2132 CAC2132 Predicted S-adenosylmethionine-dependent methyltransferase, involved in cell envelope biogenesis YLXA B.subtilis ortholog (NCBI ptt file) 201, 239
CAC2286 CAC2286 Uncharacterized protein, similar to protein from Clostridium histolyticum (GI:3892648) (NCBI ptt file) 292, 352
CAC2355 CAC2355 Hypothetical protein (NCBI ptt file) 25, 201
CAC2484 CAC2484 Predicted membrane, YQJA B.subtilis ortholog (NCBI ptt file) 47, 292
CAC2646 sipS Signal peptidase I (NCBI ptt file) 201, 295
CAC2647 CAC2647 Diverged arginase family hydrolase (NCBI ptt file) 201, 289
CAC2847 CAC2847 Ribosome-associated protein Y (PSrp-1) (NCBI ptt file) 128, 201
CAC3023 CAC3023 Hypothetical protein (NCBI ptt file) 268, 292
CAC3109 infA Translation initiation factor IF-1 (NCBI ptt file) 255, 292
CAC3113 seqY Preprotein translocase subunit SecY (NCBI ptt file) 292, 304
CAC3175 CAC3175 Hypothetical protein (NCBI ptt file) 73, 292
CAC3201 CAC3201 Formate--tetrahydrofolate ligase (NCBI ptt file) 201, 292
CAC3202 ftsH ATP-dependent Zn protease, FTSH (NCBI ptt file) 273, 292
CAC3224 purR PUR operon repressor, Adenine/guanine phosphoribosyltransferase family (NCBI ptt file) 232, 292
CAC3225 murC UDP-N-acetylmuramate-alanine ligase (NCBI ptt file) 292, 359
CAC3260 asnS Aspartyl/asparaginyl-tRNA synthetase (NCBI ptt file) 82, 292
CAC3288 CAC3288 Iron-regulated ABC transporter ATPase subunit (SufC), VEG296 B.subtilis ortholog (NCBI ptt file) 201, 296
CAC3290 CAC3290 Iron-regulated ABC-type transporter membrane component (SufB) (NCBI ptt file) 201, 209
CAC3376 CAC3376 Possible pectin degradation protein (sugar phosphate isomerase family) (NCBI ptt file) 113, 292
CAC3394 CAC3394 Uncharacterized conserved protein, YGIN family (NCBI ptt file) 232, 292
CAC3595 CAC3595 Uncharacterized FAD-dependent dehydrogenase (NCBI ptt file) 182, 292
CAC3695 CAC3695 Possible transcriptional regulator, containing DNA-binding domain of xre family (NCBI ptt file) 113, 292
CAC3739 rpmH L34 (NCBI ptt file) 201, 281
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 CAC3201
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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