Organism : Campylobacter jejuni | Module List :
Cj1243 hemE

uroporphyrinogen decarboxylase (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Uroporphyrinogen-III decarboxylase cog/ cog
uroporphyrinogen decarboxylase activity go/ molecular_function
porphyrin-containing compound biosynthetic process go/ biological_process
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
hemE tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1243
(Mouseover regulator name to see its description)

Cj1243 is regulated by 3 influences and regulates 0 modules.
Regulators for Cj1243 hemE (3)
Regulator Module Operator
Cj0400 138 tf
Cj0670 138 tf
Cj0480c 118 tf

Warning: Cj1243 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
7618 8.20e+02 Tta.AaAaAgg
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7619 1.80e+03 TTtcACtCtCacaac
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7658 7.20e+02 GGCACACC
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7659 8.80e+03 AtCaAGaG
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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 Cj1243

Cj1243 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Uroporphyrinogen-III decarboxylase cog/ cog
uroporphyrinogen decarboxylase activity go/ molecular_function
porphyrin-containing compound biosynthetic process go/ biological_process
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
hemE tigr/ tigrfam
Module neighborhood information for Cj1243

Cj1243 has total of 40 gene neighbors in modules 118, 138
Gene neighbors (40)
Gene Common Name Description Module membership
Cj0157c Cj0157c putative integral membrane protein (NCBI ptt file) 52, 118
Cj0191c def polypeptide deformylase (NCBI ptt file) 52, 118
Cj0229 Cj0229 putative acetyltransferase (NCBI ptt file) 90, 138
Cj0231c nrdB ribonucleoside-diphosphate reductase beta chain (NCBI ptt file) 133, 138
Cj0233c pyrE putative orotate phosphoribosyltransferase (NCBI ptt file) 138, 156
Cj0235c secG putative protein-export membrane protein (NCBI ptt file) 132, 138
Cj0244 rpmI 50s ribosomal protein L35 (NCBI ptt file) 138, 151
Cj0326 serC phosphoserine aminotransferase (NCBI ptt file) 41, 138
Cj0327 Cj0327 hypothetical protein Cj0327 (NCBI ptt file) 118, 138
Cj0517 crcB CRCB protein homolog (NCBI ptt file) 47, 138
Cj0578c mttB sec-independant protein translocase (NCBI ptt file) 3, 138
Cj0608 Cj0608 putative outer membrane protein (NCBI ptt file) 88, 138
Cj0651 Cj0651 putative integral membrane protein (NCBI ptt file) 6, 118
Cj0694 Cj0694 putative periplasmic protein (NCBI ptt file) 14, 118
Cj0845c gltX glutamyl-tRNA synthetase (NCBI ptt file) 18, 138
Cj0982c Cj0982c putative amino-acid transporter periplasmic solute-binding protein (NCBI ptt file) 91, 118
Cj1071 ssb single-strand DNA binding protein (NCBI ptt file) 9, 138
Cj1072 rpsR 30S ribosomal protein S18 (NCBI ptt file) 52, 138
Cj1080c Cj1080c hypothetical protein Cj1080c (NCBI ptt file) 118, 148
Cj1082c thiD phosphomethylpyrimidine kinase (NCBI ptt file) 65, 118
Cj1087c Cj1087c putative periplasmic protein (NCBI ptt file) 68, 118
Cj1089c Cj1089c hypothetical protein Cj1089c (NCBI ptt file) 18, 118
Cj1090c Cj1090c putative lipoprotein (NCBI ptt file) 65, 118
Cj1091c leuS leucyl-tRNA synthetase (NCBI ptt file) 18, 118
Cj1094c Cj1094c putative membrane protein (NCBI ptt file) 111, 118
Cj1105 smpB small protein B homolog (NCBI ptt file) 18, 138
Cj1121c wlaK putative aminotransferase (degT family) (NCBI ptt file) 118, 127
Cj1124c wlaH putative galactosyltransferase (NCBI ptt file) 109, 118
Cj1128c wlaD putative glycosyltransferase (NCBI ptt file) 118, 138
Cj1168c Cj1168c putative integral membrane protein (dedA homolog) (NCBI ptt file) 117, 138
Cj1243 hemE uroporphyrinogen decarboxylase (NCBI ptt file) 118, 138
Cj1271c tyrS tyrosyl-tRNA synthetase (NCBI ptt file) 18, 138
Cj1335 maf4 motility accessory factor (function unknown) (NCBI) 138, 166
Cj1388 Cj1388 hypothetical protein Cj1388 (NCBI ptt file) 111, 118
Cj1599 hisB imidazoleglycerol-phosphate dehydratase/histidinol-phosphatase (NCBI ptt file) 98, 138
Cj1635c rnc ribonuclease III (NCBI ptt file) 118, 140
Cj1636c rnhA ribonuclease HI (NCBI ptt file) 79, 118
Cj1645 tkt transketolase (NCBI ptt file) 70, 118
Cj1689c rplO 50S ribosomal protein L15 (NCBI ptt file) 128, 138
Cj1722c Cj1722c hypothetical protein Cj1722c (NCBI ptt file) 88, 118
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 Cj1243
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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