Organism : Methanococcus maripaludis S2 | Module List :
MMP0153 aksA

trans-homoaconitate synthase

CircVis
Functional Annotations (5)
Function System
Isopropylmalate/homocitrate/citramalate synthases cog/ cog
2-isopropylmalate synthase activity go/ molecular_function
carboxylic acid metabolic process go/ biological_process
transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer go/ molecular_function
LEU1_arch tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0153
(Mouseover regulator name to see its description)

MMP0153 is regulated by 3 influences and regulates 0 modules.
Regulators for MMP0153 aksA (3)
Regulator Module Operator
MMP0032
MMP0257
1 combiner
MMP0209 1 tf
MMP1447 1 tf

Warning: MMP0153 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
663 3.00e+01 CgacCC.c.agG
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664 7.60e+03 CcgcTg
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937 2.40e+03 GAGcGCCC
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938 4.70e+03 ccca.CAatTc.gc.AtaT
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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 MMP0153

MMP0153 is enriched for 5 functions in 3 categories.
Module neighborhood information for MMP0153

MMP0153 has total of 56 gene neighbors in modules 1, 143
Gene neighbors (56)
Gene Common Name Description Module membership
Antisense_2 None 1, 22
Antisense_23 None 1, 117
Antisense_5 None 1, 22
MMP0007 geranylgeranylglyceryl phosphate synthase-like protein 12, 143
MMP0119 birA biotin--acetyl-CoA-carboxylase ligase 1, 75, 142
MMP0145 hpt adenine phosphoribosyltransferase 137, 143
MMP0153 aksA trans-homoaconitate synthase 1, 143
MMP0154 hypothetical protein MMP0154 1, 13
MMP0166 MATE family drug/sodium antiporter 1, 28
MMP0167 ABC transporter ATP-binding protein 1, 28
MMP0168 ParR family transcriptional regulator 1, 28
MMP0176 cell division protein CDC48 1, 46
MMP0178 purQ phosphoribosylformylglycinamidine synthase I 95, 143
MMP0179 purL phosphoribosylformylglycinamidine synthase 66, 143
MMP0180 ribC riboflavin synthase 1, 58
MMP0187 thiC thiamine biosynthesis protein ThiC 137, 143
MMP0239 hypothetical protein MMP0239 1, 49, 75, 106
MMP0264 MscMJ mechanosensitive ion channel MscS 129, 143
MMP0418 carbohydrate kinase PfkB 60, 137, 143
MMP0450 ferredoxin 1, 70
MMP0451 hypothetical protein MMP0451 1, 70
MMP0536 hypothetical protein MMP0536 1, 28
MMP0540 purC phosphoribosylaminoimidazole-succinocarboxamide synthase 8, 112, 143
MMP0606 ribosomal RNA methyltransferase RrmJ/FtsJ 137, 143
MMP0607 nrpR hypothetical protein MMP0607 115, 137, 143
MMP0608 2-hydroxyglutaryl-CoA dehydratase subunit A-like protein 1, 28
MMP0685 N-6 adenine-specific DNA methylase 1, 144
MMP0697 leuS leucyl-tRNA synthetase 8, 143
MMP0698 hypothetical protein MMP0698 21, 143
MMP0876 cofG FO synthase subunit 1 1, 129
MMP0879 serS seryl-tRNA synthetase 27, 143
MMP0880 aksF isopropylmalate/isohomocitrate dehydrogenase 24, 60, 140, 143
MMP1063 leuA 2-isopropylmalate synthase 81, 143
MMP1071 hypothetical protein MMP1071 1, 106
MMP1072 aminotransferase (subgroup I) aromatic aminotransferase 1, 106
MMP1081 wbpG putative LPS biosynthesis protein WbpG 137, 143
MMP1082 hisH imidazole glycerol phosphate synthase subunit HisH 66, 143
MMP1083 imidazole glycerol phosphate synthase subunit HisF 137, 143
MMP1085 hypothetical protein MMP1085 141, 143, 149
MMP1122 translation-associated GTPase 137, 143
MMP1140 fdxA ferredoxin 1, 46
MMP1146 purF amidophosphoribosyltransferase 7, 60, 137, 143
MMP1185 hydrogen uptake protein:hydrogenase maturation protease HycI 1, 46
MMP1198 nitrate/sulfonate/bicarbonate ABC transporter ATPase 12, 143
MMP1238 bioB biotin synthase 1, 153
MMP1240 Sep-tRNA:Cys-tRNA synthetase 1, 55
MMP1241 hypothetical protein MMP1241 1, 55, 94, 117
MMP1496 pheS phenylalanyl-tRNA synthetase subunit alpha 137, 143
MMP1549 AP endonuclease 1, 94, 152
MMP1550 NADP oxidoreductase, coenzyme F420-dependent 1, 58
MMP1592 trpS tryptophanyl-tRNA synthetase 27, 143
MMP1594 hypothetical protein MMP1594 51, 143
MMP1605 pyruvate kinase 1, 54, 146, 166
MMP1606 flavoprotein:DNA/pantothenate metabolism flavoprotein 1, 13, 49
MMP1681 hypothetical protein MMP1681 21, 143
Unanno_24 None 95, 143
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 MMP0153
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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