Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0699 hemZ

Anaerobic coproporphyrinogen oxidase (HemZ) (NCBI)

CircVis
Functional Annotations (10)
Function System
Coproporphyrinogen III oxidase and related Fe-S oxidoreductases cog/ cog
coproporphyrinogen oxidase activity go/ molecular_function
cytoplasm go/ cellular_component
porphyrin-containing compound biosynthetic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
coproporphyrinogen dehydrogenase activity go/ molecular_function
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
hemN tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0699
(Mouseover regulator name to see its description)

RSP_0699 is regulated by 13 influences and regulates 0 modules.
Regulators for RSP_0699 hemZ (13)
Regulator Module Operator
RSP_0443 78 tf
RSP_2346 78 tf
RSP_2888 78 tf
RSP_3238 78 tf
RSP_3341 78 tf
RSP_0547 275 tf
RSP_0698 275 tf
RSP_1486 275 tf
RSP_2346 275 tf
RSP_2888 275 tf
RSP_2963 275 tf
RSP_3238 275 tf
RSP_3341 275 tf

Warning: RSP_0699 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
7876 3.00e-01 tTGAtCtGcaTCAAa
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7877 1.40e+04 caCcCacaATC
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8264 6.50e-15 ttAatgccTTGAcctacATCAA
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8265 2.60e-01 aaccTCacaTGtCt
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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 RSP_0699

RSP_0699 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Coproporphyrinogen III oxidase and related Fe-S oxidoreductases cog/ cog
coproporphyrinogen oxidase activity go/ molecular_function
cytoplasm go/ cellular_component
porphyrin-containing compound biosynthetic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
coproporphyrinogen dehydrogenase activity go/ molecular_function
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
hemN tigr/ tigrfam
Module neighborhood information for RSP_0699

RSP_0699 has total of 30 gene neighbors in modules 78, 275
Gene neighbors (30)
Gene Common Name Description Module membership
RSP_0166 dksA DnaK suppressor protein (NCBI) 78, 275
RSP_0317 hemN Coproporphyrinogen III oxidase, oxygen-independent (HemN) (NCBI) 78, 275
RSP_0464 RSP_0464 putative protease (NCBI) 201, 275
RSP_0465 RSP_0465 putative protease (NCBI) 201, 275
RSP_0466 RSP_0466 hypothetical protein (NCBI) 201, 275
RSP_0467 ubiD 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (NCBI) 201, 275
RSP_0468 RSP_0468 putative 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (NCBI) 275, 358
RSP_0699 hemZ Anaerobic coproporphyrinogen oxidase (HemZ) (NCBI) 78, 275
RSP_0775 RSP_0775 Class I monoheme cytochrome c (NCBI) 78, 382
RSP_0820 RSP_0820 Putative cytochrome B561 (NCBI) 45, 275
RSP_1255 RSP_1255 Phosphate acetyl/butaryl transferase (NCBI) 270, 275
RSP_1256 RSP_1256 putative NADH-enoyl acyl carrier protein reductase (NCBI) 270, 275
RSP_1257 phbC putative polyhydroxyalkanoic synthase, PHA synthase (NCBI) 270, 275
RSP_1714 tufA Elongation factor TU (NCBI) 78, 321
RSP_2176C gabT Aminotransferase class-III; Carboxyl-terminus fragment (NCBI) 8, 275
RSP_2176N gabT Aminotransferase class-III; Amino-terminus fragment (NCBI) 275, 283
RSP_2247 fusA putative translation elongation factor (NCBI) 78, 382
RSP_2337 RSP_2337 hypothetical protein (NCBI) 78, 382
RSP_6016 RSP_6016 hypothetical protein (NCBI) 78, 123
RSP_6017 rpsQ Ribosomal protein S17 (NCBI) 78, 321
RSP_6067 RSP_6067 hypothetical protein (NCBI) 275, 295
RSP_6120 RSP_6120 hypothetical protein (NCBI) 8, 78
RSP_6125 RSP_6125 hypothetical protein (NCBI) 78, 123
RSP_6151 RSP_6151 hypothetical protein (NCBI) 257, 275
RSP_6165 RSP_6165 transcriptional regulator, LysR family (NCBI) 275, 330
RSP_6187 RSP_6187 hypothetical protein (NCBI) 275, 276
RSP_6200 RSP_6200 hypothetical protein (NCBI) 78, 283
RSP_6207 RSP_6207 hypothetical protein (NCBI) 78, 352
RSP_6214 trpC indole-3-glycerol phosphate synthase (NCBI) 50, 78
RSP_6246 RSP_6246 bacteriophage head-tail adaptor (NCBI) 78, 131
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 RSP_0699
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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