Organism : Bacillus subtilis | Module List :
BSU28170 hemA

glutamyl-tRNA reductase (RefSeq)

CircVis
Functional Annotations (10)
Function System
Glutamyl-tRNA reductase cog/ cog
shikimate 3-dehydrogenase (NADP+) activity go/ molecular_function
cytoplasm go/ cellular_component
glutamyl-tRNA reductase activity go/ molecular_function
tetrapyrrole biosynthetic process go/ biological_process
NADP binding go/ molecular_function
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
hemA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU28170
(Mouseover regulator name to see its description)

BSU28170 is regulated by 17 influences and regulates 0 modules.
Regulators for BSU28170 hemA (17)
Regulator Module Operator
BSU00330 173 tf
BSU08520 173 tf
BSU14240 173 tf
BSU29000 173 tf
BSU40410 173 tf
BSU40960 173 tf
BSU40970 173 tf
BSU02070 237 tf
BSU04680 237 tf
BSU09560 237 tf
BSU16810 237 tf
BSU25760 237 tf
BSU29110 237 tf
BSU31530 237 tf
BSU33950 237 tf
BSU37550 237 tf
BSU40410 237 tf

Warning: BSU28170 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
5294 1.50e+05 taTaatATa.gAAtgagAaa
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5295 1.90e+04 AGGgGG
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5416 1.10e+02 TgtTAaaataattAaAgaaa
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5417 6.60e+02 CAcCgCC.tCAtCAc
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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 BSU28170

BSU28170 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Glutamyl-tRNA reductase cog/ cog
shikimate 3-dehydrogenase (NADP+) activity go/ molecular_function
cytoplasm go/ cellular_component
glutamyl-tRNA reductase activity go/ molecular_function
tetrapyrrole biosynthetic process go/ biological_process
NADP binding go/ molecular_function
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
hemA tigr/ tigrfam
Module neighborhood information for BSU28170

BSU28170 has total of 42 gene neighbors in modules 173, 237
Gene neighbors (42)
Gene Common Name Description Module membership
BSU00300 yaaR hypothetical protein (RefSeq) 54, 173
BSU00310 holB DNA polymerase III subunit delta' (RefSeq) 54, 173
BSU00330 yabA DNA replication intiation control protein YabA (RefSeq) 54, 173
BSU03900 gabT 4-aminobutyrate aminotransferase (RefSeq) 173, 231
BSU06840 yeeI hypothetical protein (RefSeq) 173, 327
BSU08820 katA vegetative catalase 1 (RefSeq) 49, 237
BSU13970 ykwD hypothetical protein (RefSeq) 121, 173
BSU14240 rok repressor of comK (RefSeq) 35, 173
BSU14440 ykpB 2-dehydropantoate 2-reductase (RefSeq) 170, 173
BSU14490 kinC two-component sensor histidine kinase (RefSeq) 173, 219
BSU15390 sepF cell division machinery factor (RefSeq) 237, 402
BSU23160 rluB pseudouridine synthase (RefSeq) 173, 284
BSU25340 phoH phosphate starvation-induced protein (RefSeq) 173, 220
BSU26350 yqaE putative transcriptional regulator (Xre family); skin element (RefSeq) 35, 173
BSU28120 hemL glutamate-1-semialdehyde aminotransferase (RefSeq) 188, 237
BSU28130 hemB delta-aminolevulinic acid dehydratase (RefSeq) 188, 237
BSU28140 hemD uroporphyrinogen III cosynthase (RefSeq) 188, 237
BSU28150 hemC porphobilinogen deaminase (RefSeq) 188, 237
BSU28160 hemX negative effector of the concentration of glutamyl-tRNA reductase HemA (RefSeq) 188, 237
BSU28170 hemA glutamyl-tRNA reductase (RefSeq) 173, 237
BSU28460 yslB hypothetical protein (RefSeq) 173, 315
BSU31800 yueF putative integral inner membrane protein (RefSeq) 23, 237
BSU32670 sufB FeS cluster formation protein (RefSeq) 237, 324
BSU32680 iscU iron-sulfur cluster assembly scaffold protein (RefSeq) 237, 324
BSU32690 sufS cysteine desulfurase (RefSeq) 237, 324
BSU32700 sufD FeS assembly protein SufD (RefSeq) 237, 324
BSU32710 sufC sulfur mobilizing ABC protein, ATPase (RefSeq) 237, 324
BSU33940 gapA glyceraldehyde-3-phosphate dehydrogenase (RefSeq) 237, 355
BSU33950 cggR transcriptional regulator of gapA (RefSeq) 237, 388
BSU35300 secA preprotein translocase subunit SecA (RefSeq) 237, 388
BSU36000 alsD alpha-acetolactate decarboxylase (RefSeq) 237, 341
BSU36010 alsS acetolactate synthase (RefSeq) 237, 341
BSU36380 rapD response regulator aspartate phosphatase (RefSeq) 91, 237
BSU36700 moaA molybdenum cofactor biosynthesis protein A (RefSeq) 160, 237
BSU36710 fdhD formate dehydrogenase accessory protein (RefSeq) 160, 237
BSU36930 ywlE protein-tyrosine-phosphatase (RefSeq) 237, 334
BSU37520 ywhD hypothetical protein (RefSeq) 82, 237
BSU37530 ywhC putative metal-dependent hydrolase; integral inner membrane protein (RefSeq) 82, 237
BSU40090 ahpC alkyl hydroperoxide reductase (small subunit) (RefSeq) 237, 324
BSU40100 ahpF alkyl hydroperoxide reductase (large subunit) (RefSeq) 237, 324
BSU40960 parB site-specific DNA-binding protein (RefSeq) 169, 173
BSU40970 parA chromosome partitioning protein; transcriptional regulator (RefSeq) 169, 173
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 BSU28170
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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