Organism : Clostridium acetobutylicum | Module List :
CAC0256 nifD

Nitrogenase molybdenum-iron protein, alpha chain (nitrogenase component I) gene nifD (NCBI ptt file)

CircVis
Functional Annotations (12)
Function System
Nitrogenase molybdenum-iron protein, alpha and beta chains cog/ cog
electron transport go/ biological_process
nitrogen fixation go/ biological_process
nitrogenase activity go/ molecular_function
iron-iron nitrogenase complex go/ cellular_component
molybdenum-iron nitrogenase complex go/ cellular_component
vanadium-iron nitrogenase complex go/ cellular_component
iron-iron nitrogenase activity go/ molecular_function
molybdenum-iron nitrogenase activity go/ molecular_function
vanadium-iron nitrogenase activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
nifD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0256
(Mouseover regulator name to see its description)

CAC0256 is regulated by 19 influences and regulates 0 modules.
Regulators for CAC0256 nifD (19)
Regulator Module Operator
CAC0254 98 tf
CAC0255 98 tf
CAC0863 98 tf
CAC1668 98 tf
CAC1698 98 tf
CAC1928 98 tf
CAC2236 98 tf
CAC3267 98 tf
CAC0144 347 tf
CAC0254 347 tf
CAC0255 347 tf
CAC1698 347 tf
CAC1766 347 tf
CAC1928 347 tf
CAC1941 347 tf
CAC2236 347 tf
CAC3472 347 tf
CAC3475 347 tf
CAC3525 347 tf

Warning: CAC0256 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
6848 3.10e-07 ttggAGGagga
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6849 1.40e+03 AcGtaAaAgccggATgG
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7346 1.40e-02 AGGaGg
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7347 1.30e+03 cataagt..caGAAg.caca
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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 CAC0256

CAC0256 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
Nitrogenase molybdenum-iron protein, alpha and beta chains cog/ cog
electron transport go/ biological_process
nitrogen fixation go/ biological_process
nitrogenase activity go/ molecular_function
iron-iron nitrogenase complex go/ cellular_component
molybdenum-iron nitrogenase complex go/ cellular_component
vanadium-iron nitrogenase complex go/ cellular_component
iron-iron nitrogenase activity go/ molecular_function
molybdenum-iron nitrogenase activity go/ molecular_function
vanadium-iron nitrogenase activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
nifD tigr/ tigrfam
Module neighborhood information for CAC0256

CAC0256 has total of 35 gene neighbors in modules 98, 347
Gene neighbors (35)
Gene Common Name Description Module membership
CAC0020 CAC0020 MDR-type permease (NCBI ptt file) 98, 175
CAC0042 CAC0042 Hypothetical protein, CF-1 family (NCBI ptt file) 129, 347
CAC0206 CAC0206 Uncharacterized conserved membrane protein (NCBI ptt file) 98, 150
CAC0253 nifH Nitrogenase iron protein (nitrogenase component II) gene nifH (NCBI ptt file) 98, 320
CAC0255 nifHD Nitrogen regulatory protein PII (nitrogen fixation nifHD) (NCBI ptt file) 98, 144
CAC0256 nifD Nitrogenase molybdenum-iron protein, alpha chain (nitrogenase component I) gene nifD (NCBI ptt file) 98, 347
CAC0258 nifE Nitrogenase iron-molibdenum cofactor biosinthesis protein, gene nifE (NCBI ptt file) 161, 347
CAC0363 CAC0363 Deoxyinosine 3'endonuclease (NCBI ptt file) 333, 347
CAC0544 CAC0544 Permease (NCBI ptt file) 98, 347
CAC0564 CAC0564 Response regulator (REC, HTH domains) (NCBI ptt file) 101, 347
CAC0565 CAC0565 Histidine kinase (HAMP, HisKA and HATPase domains) (NCBI ptt file) 101, 347
CAC0759 CAC0759 Hypothetical protein (NCBI ptt file) 98, 338
CAC0794 CAC0794 Nucleoside-diphosphate-sugar epimerase (UDP-glucose 4-epimerase) (NCBI ptt file) 98, 320
CAC0829 CAC0829 Uncharacterized conserved membrane protein, similar to MDR (VANZ) ORF of Enterococcus (NCBI ptt file) 98, 175
CAC1462 CAC1462 Levanase/invertase (NCBI ptt file) 98, 320
CAC1534 CAC1534 Predicted permease (NCBI ptt file) 307, 347
CAC1535 CAC1535 ABC transporter, ATPase component (NCBI ptt file) 101, 347
CAC1773 sacC Levanase (NCBI ptt file) 98, 357
CAC2047 CAC2047 Conjugative transfer gene TrsE homolog, ATPase (NCBI ptt file) 161, 347
CAC2674 CAC2674 ATP-dependent superfamily I DNA helicase, PCRA (NCBI ptt file) 3, 98
CAC2707 CAC2707 8-oxoguanine-DNA-glycosylase (NCBI ptt file) 98, 343
CAC2731 CAC2731 Predicted permease (NCBI ptt file) 98, 343
CAC2734 CAC2734 ABC-type multidrug transport system, ATPase component (NCBI ptt file) 71, 98
CAC2736 sbcC ATPase involved in DNA repair (NCBI ptt file) 91, 98
CAC2862 murA UDP-N-acetylglucosamine 1-carboxyvinyltransferase (NCBI ptt file) 78, 98
CAC3304 CAC3304 Hypothetical protein, CF-42 family (NCBI ptt file) 22, 98
CAC3337 CAC3337 Predicted amidohodrolase (dihydroorotase family) (NCBI ptt file) 320, 347
CAC3498 CAC3498 Sugar kinase, ribokinase family (NCBI ptt file) 98, 175
CAC3499 CAC3499 Predicted endonuclease (NCBI ptt file) 98, 338
CAC3514 CAC3514 Reverse transcriptase/maturase family protein (NCBI ptt file) 101, 347
CAC3521 CAC3521 Hypothetical protein (NCBI ptt file) 101, 347
CAC3522 CAC3522 Hypothetical protein, CF-7 family (NCBI ptt file) 226, 347
CAC3582 CAC3582 Hypothetical protein (NCBI ptt file) 98, 103
CAC3585 CAC3585 ABC-type transporter, ATPase component (NCBI ptt file) 98, 103
CAC3698 CAC3698 Hypothetical protein, CF-44 family (NCBI ptt file) 101, 347
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 CAC0256
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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