Category: kegg

KEGG ENZYME: 1.1.1.124

KEGG ENZYME: 1.1.1.124     ENZYME: 1.1.1.124 Help Entry EC 1.1.1.124                Enzyme                                  Name fructose 5-dehydrogenase (NADP+);5-ketofructose reductase (NADP+);5-keto-D-fructose reductase (NADP+);fructose 5-(nicotinamide adenine dinucleotide phosphate) dehydrogenase;D-(-)fructose:(NADP+) 5-oxidoreductase;fructose 5-dehydrogenase (NADP+) Class Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptorBRITE hierarchy Sysname D-fructose:NADP+ 5-oxidoreductase Reaction(IUBMB) D-fructose + NADP+ = 5-dehydro-D-fructose + NADPH…

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KEGG ENZYME: 1.7.2.7

Entry EC 1.7.2.7                  Enzyme                                  Name Class Oxidoreductases;Acting on other nitrogenous compounds as donors;With a cytochrome as acceptorBRITE hierarchy Sysname hydrazine:ferricytochrome-c oxidoreductase Reaction(IUBMB) hydrazine + H2O + 3 ferricytochrome c = nitric oxide + ammonium + 3 ferrocytochrome c [RN:R09799] Reaction(KEGG) Substrate Product nitric oxide [CPD:C00533]; ammonium; ferrocytochrome c [CPD:C00126] Comment The enzyme,…

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kegg IDs to pathways in R

kegg IDs to pathways in R 0 Hi all, I have never done this before but i suspect there must be an easy way to convert KEGG ids to pathways in R. I have a dataframe containing info from 1000 sth bacterial genomes; their taxonomy, their orfs and the kegg…

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KEGG ENZYME: 1.1.3.39

KEGG ENZYME: 1.1.3.39     ENZYME: 1.1.3.39 Help Entry EC 1.1.3.39                 Enzyme                                  Name nucleoside oxidase (H2O2-forming) Class Oxidoreductases;Acting on the CH-OH group of donors;With oxygen as acceptorBRITE hierarchy Sysname nucleoside:oxygen 5′-oxidoreductase (H2O2-forming) Reaction(IUBMB) adenosine + 2 O2 + H2O = 9-riburonosyladenine + 2 H2O2 (overall reaction) [RN:R05695]; (1a) adenosine + O2 = 5′-dehydroadenosine…

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KEGG ENZYME: 2.1.4.1

Entry EC 2.1.4.1                  Enzyme                                  Name glycine amidinotransferase;arginine-glycine amidinotransferase;arginine-glycine transamidinase;glycine transamidinase Class Transferases;Transferring one-carbon groups;AmidinotransferasesBRITE hierarchy Sysname L-arginine:glycine amidinotransferase Reaction(IUBMB) L-arginine + glycine = L-ornithine + guanidinoacetate [RN:R00565] Reaction(KEGG) Substrate Product Comment Canavanine can act instead of arginine. History EC 2.1.4.1 created 1961 as EC 2.6.2.1, transferred 1965 to EC 2.1.4.1 Pathway ec00260  …

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KEGG ENZYME: 1.4.1.4

Entry EC 1.4.1.4                  Enzyme                                  Name glutamate dehydrogenase (NADP+);glutamic dehydrogenase;dehydrogenase, glutamate (nicotinamide adenine dinucleotide (phosphate));glutamic acid dehydrogenase;L-glutamate dehydrogenase;L-glutamic acid dehydrogenase;NAD(P)+-glutamate dehydrogenase;NAD(P)H-dependent glutamate dehydrogenase;glutamate dehydrogenase (NADP+) Class Oxidoreductases;Acting on the CH-NH2 group of donors;With NAD+ or NADP+ as acceptorBRITE hierarchy Sysname L-glutamate:NADP+ oxidoreductase (deaminating) Reaction(IUBMB) L-glutamate + H2O + NADP+ = 2-oxoglutarate + NH3…

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KEGG ENZYME: 2.5.1.84

Entry EC 2.5.1.84                 Enzyme                                  Name all-trans-nonaprenyl diphosphate synthase [geranyl-diphosphate specific];nonaprenyl diphosphate synthase (ambiguous);solanesyl diphosphate synthase (ambiguous);SolPP synthase (ambiguous);SPP-synthase (ambiguous);SPP synthase (ambiguous);solanesyl-diphosphate synthase (ambiguous);OsSPS2 Class Transferases;Transferring alkyl or aryl groups, other than methyl groups;Transferring alkyl or aryl groups, other than methyl groups (only sub-subclass identified to date)BRITE hierarchy Sysname geranyl-diphosphate:isopentenyl-diphosphate transtransferase (adding 7…

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Practical value of bits and SW-score in KEGG

Practical value of bits and SW-score in KEGG 1 Hello, Can someone explain to me the practical value of bits and SW-score in KEGG? What does it actually mean for my sequence? The image below shows paralogs table as shown in the base what is the practical value of these…

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Pathway enrichment analysis

Pathway enrichment analysis 1 Hi! I have found DEGs. What do I use for the pathway enrichment analysis; all DEGs or separate between up and down? Also is it normal to only choose a subset like the top 50 up-reg genes or would I like to take all the up-reg…

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KEGG ENZYME: 3.5.1.12

Entry EC 3.5.1.12                 Enzyme                                  Name biotinidase;amidohydrolase biotinidase Class Hydrolases;Acting on carbon-nitrogen bonds, other than peptide bonds;In linear amidesBRITE hierarchy Sysname biotin-amide amidohydrolase Reaction(IUBMB) biotin amide + H2O = biotin + NH3 [RN:R01076] Reaction(KEGG) Substrate Product Comment Also acts on biotin esters. History EC 3.5.1.12 created 1961 Pathway Orthology Genes  » show allTaxonomy…

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ANGPTL8/betatrophin improves glucose tolerance | DMSO

Introduction Insulin resistance is a major risk factor for metabolic syndrome (MetS), including type 2 diabetes mellitus (T2DM).1 T2DM is characterized by insulin resistance in the liver.2 Insulin resistance is an abnormal physiological state that occurs when cells are unable to use insulin effectively, leading to T2DM, a major health…

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How to get a list of all KEGG ko terms vs names?

How to get a list of all KEGG ko terms vs names? 2 I want to map a list of KEGG terms with their corresponding names. Is it possible to get a list of all KEGG terms and their descriptions/names? kegg annotation rna-seq • 1.0k views Hi. I am not…

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KEGG COMPOUND: C01771

KEGG COMPOUND: C01771     COMPOUND: C01771 Help Entry C01771                      Compound                                Name 2-Butenoate;2-Butenoic acid;Crotonic acid;3-Methylacrylic acid Formula C4H6O2 Exact mass 86.0368 Mol weight 86.0892 Structure Mol fileKCF fileDB search Reaction Enzyme Other DBs KCF data Show ATOM        6            1   C2b C    22.1306  -15.0946            2   C6a C    23.3400  -15.7959            3   C2b C    20.9148  -15.7959            4   O6a O    23.3400  -17.4782            5   O6a O    24.5495  -15.0946            6   C1a C    19.7053  -15.0946BOND        5            1     1   2 1            2     1   3 2            3     2   4 1            4     2   5 2            5     3   6 1 » Japanese version DBGET…

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Summary of KEGG functional categories from an annotated genome? Is there a tool for this?

Summary of KEGG functional categories from an annotated genome? Is there a tool for this? 0 I have several annotated bacterial genomes that I have been analyzing. I have run them through the web-browser utility BlastKOALA to get KEGG functional annotations. This generates a list of KO numbers and allows…

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KEGG ENZYME: 2.3.1.13

Entry EC 2.3.1.13                 Enzyme                                  Name glycine N-acyltransferase;glycine acyltransferase;glycine-N-acylase Class Transferases;Acyltransferases;Transferring groups other than aminoacyl groupsBRITE hierarchy Sysname acyl-CoA:glycine N-acyltransferase Reaction(IUBMB) acyl-CoA + glycine = CoA + N-acylglycine [RN:R00395] Reaction(KEGG) Substrate Product Comment The CoA derivatives of a number of aliphatic and aromatic acids, but not phenylacetyl-CoA or (indol-3-yl)acetyl-CoA, can act as donor….

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Biocmanager Install Vs Install Packages

Introduction to RNAseq I Day 3 Nicolas Rochette (EEB/ISG, UCLA) Karolina Kaczor-Urbanowicz (Oral Biology & Medicine, UCLA) UCLA Institute for Quantitative and Computational BiologyOver-representation (or enrichment) analysis is a statistical method that determines whether genes from pre-defined sets (ex: those beloging to a specific GO term or KEGG pathway) are…

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KEGG ENZYME: 2.7.7.78

Entry EC 2.7.7.78                 Enzyme                                  Name GDP-D-glucose phosphorylase Class Transferases;Transferring phosphorus-containing groups;NucleotidyltransferasesBRITE hierarchy Sysname GDP:alpha-D-glucose 1-phosphate guanylyltransferase Reaction(IUBMB) GDP-alpha-D-glucose + phosphate = alpha-D-glucose 1-phosphate + GDP [RN:R09752] Reaction(KEGG) R09752 Reaction Substrate GDP-alpha-D-glucose [CPD:C00394]; phosphate [CPD:C00009] Product alpha-D-glucose 1-phosphate [CPD:C00103]; GDP [CPD:C00035] Comment The enzyme may be involved in prevention of misincorporation of glucose…

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KEGG REACTION: R00713

Entry R00713                      Reaction                                Name succinate-semialdehyde:NAD+ oxidoreductase Definition Succinate semialdehyde + NAD+ + H2O <=> Succinate + NADH + H+ Equation Comment Reaction class Enzyme Pathway rn00250   Alanine, aspartate and glutamate metabolism rn00760   Nicotinate and nicotinamide metabolism rn01120   Microbial metabolism in diverse environments Module M00027   GABA (gamma-Aminobutyrate) shunt Orthology K17761   succinate-semialdehyde dehydrogenase,…

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Gene Set Enrichment Analysis, KEGG and over representative analysis

Dear Seniors, I am looking to perform GSEA, KEGG and Over Representative Analysis. I found ClusterProfiler interesting and had ago with “GO classification” including groupGo (gene classification based on GO distribution at a specific level) , enrichGO (Over Representative analysis), gseGO (GO Gene Set Enrichment Analysis). ClusterProfiler needs EntrezID. Unfortunately,…

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KEGG ENZYME: 1.14.14.39

Entry EC 1.14.14.39               Enzyme                                  Name isoleucine N-monooxygenase;CYP79D3 (gene name);CYP79D4 (gene name) Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donorBRITE hierarchy Sysname L-isoleucine,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (N-hydroxylating) Reaction(IUBMB) L-isoleucine + 2…

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KEGG ENZYME: 6.3.2.6

Entry EC 6.3.2.6                  Enzyme                                  Name phosphoribosylaminoimidazolesuccinocarboxamide synthase;phosphoribosylaminoimidazole-succinocarboxamide synthetase;PurC;SAICAR synthetase;4-(N-succinocarboxamide)-5-aminoimidazole synthetase;4-[(N-succinylamino)carbonyl]-5-aminoimidazole ribonucleotide synthetase;SAICARs;phosphoribosylaminoimidazolesuccinocarboxamide synthetase;5-aminoimidazole-4-N-succinocarboxamide ribonucleotide synthetase Class Ligases;Forming carbon-nitrogen bonds;Acid-D-amino-acid ligases (peptide synthases)BRITE hierarchy Sysname 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate:L-aspartate ligase (ADP-forming) Reaction(IUBMB) ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate = ADP + phosphate + (S)-2-[5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate [RN:R04591] Reaction(KEGG) Substrate ATP [CPD:C00002]; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate [CPD:C04751]; L-aspartate [CPD:C00049] Product ADP [CPD:C00008]; phosphate…

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All samples have 0 counts for all genes. check the counting script

DESeq2: All samples have 0 counts for all genes. check the counting script 1 @2f3f6904 Last seen 1 hour ago United Kingdom I am having problems importing my HTSeq count data- it tells me the counts are zero when this is clearly not the case when head outputs: >head(WTCHG_862660_71955267) GeneID…

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visualisation of proteomics data using r and bioconductor

R package version 0.99.7, 2014. [9] have developed an approach to estimate peptide isoelectric point values using a Support Vector Machine classifier from the caret package [10]. [73] De Duve, C., Beaufay, H., A Short History of Tissue Fractionation. The readers are referred to the respective documentation and vignettes for…

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entry level bioinformatics jobs

New York City, New York (US) $50,000.00 – $150,000.00 per annum. Level. Found inside – Page 394Entry-level talents will then be sufficiently qualified to operate the … or run a bioinformatics tool package, one needs training, not education. With a Doctorate degree, bioinformatics assistants earn a median annual income of…

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KEGG ENZYME: 2.7.1.90

Entry EC 2.7.1.90                 Enzyme                                  Name diphosphate—fructose-6-phosphate 1-phosphotransferase;6-phosphofructokinase (pyrophosphate);pyrophosphate-fructose 6-phosphate 1-phosphotransferase;inorganic pyrophosphate-dependent phosphofructokinase;inorganic pyrophosphate-phosphofructokinase;pyrophosphate-dependent phosphofructo-1-kinase;pyrophosphate-fructose 6-phosphate phosphotransferase Class Transferases;Transferring phosphorus-containing groups;Phosphotransferases with an alcohol group as acceptorBRITE hierarchy Sysname diphosphate:D-fructose-6-phosphate 1-phosphotransferase Reaction(IUBMB) diphosphate + D-fructose 6-phosphate = phosphate + D-fructose 1,6-bisphosphate [RN:R00764] Reaction(KEGG) Substrate diphosphate [CPD:C00013]; D-fructose 6-phosphate [CPD:C00085] Product phosphate [CPD:C00009]; D-fructose…

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GO enrichment and KEGG output empty

Hello Comunity, Using DeSeq2, I have obtained the list of genes which are differentially expressed across my samples. This analysis finished with 2 files: (1) ent_gene (or gene_1) and (2) ent_uni (or uni_1). The first one corresponds with the list of genes diff. expressed, and the second one is with…

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Can DESeq2 be applied on gene coverages, rather than read counts?

Can DESeq2 be applied on gene coverages, rather than read counts? 0 Hello everyone, I have 18 soil metagenomes sampled from three different conditions (6 samples each), for which I have assembled. I’d like to do a comparative study of the genes that could potentially be expressed in these samples….

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KEGG ENZYME: 1.3.98.1

Entry EC 1.3.98.1                 Enzyme                                  Name dihydroorotate dehydrogenase (fumarate);DHOdehase (ambiguous);dihydroorotate dehydrogenase (ambiguous);dihydoorotic acid dehydrogenase (ambiguous);DHOD (ambiguous);DHODase (ambiguous);dihydroorotate oxidase;pyr4 (gene name) Class Oxidoreductases;Acting on the CH-CH group of donors;With other, known, physiological acceptorsBRITE hierarchy Sysname (S)-dihydroorotate:fumarate oxidoreductase Reaction(IUBMB) (S)-dihydroorotate + fumarate = orotate + succinate [RN:R01867] Reaction(KEGG) Substrate Product Comment Binds FMN. The reaction,…

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KEGG ENZYME: 3.1.3.89

Entry EC 3.1.3.89                 Enzyme                                  Name 5′-deoxynucleotidase;yfbR (gene name) Class Hydrolases;Acting on ester bonds;Phosphoric-monoester hydrolasesBRITE hierarchy Sysname 2′-deoxyribonucleoside 5′-monophosphate phosphohydrolase Reaction(IUBMB) a 2′-deoxyribonucleoside 5′-monophosphate + H2O = a 2′-deoxyribonucleoside + phosphate [RN:R10776] Reaction(KEGG) Substrate 2′-deoxyribonucleoside 5′-monophosphate [CPD:C00676]; H2O [CPD:C00001] Product Comment The enzyme, characterized from the bacterium Escherichia coli, shows strict specificity towards…

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KEGG ENZYME: 3.6.1.22

Entry EC 3.6.1.22                 Enzyme                                  Name NAD+ diphosphatase;NPY1 (gene name);nudC (gene name);NUDT7 (gene name);nicotinamide adenine dinucleotide pyrophosphatase;NADP pyrophosphatase;NADH pyrophosphatase;NAD+ phosphohydrolase Class Hydrolases;Acting on acid anhydrides;In phosphorus-containing anhydridesBRITE hierarchy Sysname NAD(H) phosphohydrolase Reaction(IUBMB) Reaction(KEGG) Substrate Product Comment This enzyme, described from plants, animals, and bacteria, can act on both reduced and oxidized forms of…

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Bioconductor – Melissa

DOI: 10.18129/B9.bioc.Melissa     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Melissa. Bayesian clustering and imputationa of single cell methylomes Bioconductor version: 3.9 Melissa is a Baysian probabilistic model for jointly clustering and imputing single cell methylomes. This is done by taking…

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Biopython Biopython Statistics & Issues

Issue Title State Comments Created Date Updated Date Closed Date Add .islower() and .isupper() methods to Seq? open 0 2021-09-25 2021-09-18 – Apparently random fluctuations in coverage via CodeCov? open 1 2021-09-23 2021-09-18 – BgzfWriter accepts read-only fileobj open 1 2021-09-23 2021-09-18 – BgzfReader argument `mode` not tested if a…

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How to load output from the kegg API in biopython into a pandas dataframe?

solution from @sören: I came up with this solution for my problem: from Bio.KEGG import REST as kegg def _get_kegg(kegg_id): kegg_output = kegg.kegg_get(kegg_id).read() results = {} for line in kegg_output.split(‘n’): splits = line.split() if not line.startswith(‘ ‘): if len(splits) > 0: key = splits[0] value=” “.join(splits[1:]) results[key] = value else:…

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KEGG ENZYME: 2.6.1.52

Entry EC 2.6.1.52                 Enzyme                                  Name phosphoserine transaminase;PSAT;phosphoserine aminotransferase;3-phosphoserine aminotransferase;hydroxypyruvic phosphate-glutamic transaminase;L-phosphoserine aminotransferase;phosphohydroxypyruvate transaminase;phosphohydroxypyruvic-glutamic transaminase;3-O-phospho-L-serine:2-oxoglutarate aminotransferase;SerC;PdxC;3PHP transaminase Class Transferases;Transferring nitrogenous groups;TransaminasesBRITE hierarchy Sysname O-phospho-L-serine:2-oxoglutarate aminotransferase Reaction(IUBMB) (1) O-phospho-L-serine + 2-oxoglutarate = 3-phosphooxypyruvate + L-glutamate [RN:R04173]; (2) 4-phosphooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate [RN:R05085] Reaction(KEGG) Substrate O-phospho-L-serine [CPD:C01005]; 2-oxoglutarate [CPD:C00026]; 4-phosphooxy-L-threonine [CPD:C06055] Product…

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KEGG ENZYME: 2.2.1.3

Entry EC 2.2.1.3                  Enzyme                                  Name formaldehyde transketolase;dihydroxyacetone synthase Class Transferases;Transferring aldehyde or ketonic groups;Transketolases and transaldolasesBRITE hierarchy Sysname D-xylulose-5-phosphate:formaldehyde glycolaldehydetransferase Reaction(IUBMB) D-xylulose 5-phosphate + formaldehyde = D-glyceraldehyde 3-phosphate + glycerone [RN:R01440] Reaction(KEGG) Substrate D-xylulose 5-phosphate [CPD:C00231]; formaldehyde [CPD:C00067] Product D-glyceraldehyde 3-phosphate [CPD:C00118]; glycerone [CPD:C00184] Comment A thiamine-diphosphate protein. Not identical with EC…

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Bioconductor – eisa

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see eisa. Expression data analysis via the Iterative Signature Algorithm Bioconductor version: 2.9 The Iterative Signature Algorithm (ISA) is a biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular)…

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Extracting The Features From Genbank File

Hi I have a set of the genes (mouse) for which i would like to get the function, tissue specificity and other features. I have obtained a file (.dat) from uniprot which has all such information. but it also has unwanted information. The data seems to be in genbank format….

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miRNAs and mRNAs in intestinal ischemia-reperfusion injury

Introduction Intestinal ischemia-reperfusion (II/R) injury is a severe clinical complication common in the Intensive Care Unit (ICU). It is associated with high morbidity and mortality.1 Usually, this problem is followed by various causes, including sepsis, shock, trauma, and so on.2 Intestinal ischemia-reperfusion injury destroys intestinal tissue and impairs the function…

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clusterProfiler won’t read gene list

clusterProfiler won’t read gene list 0 So I have a list of DE genes that I would like to analyse for enriched GO and KEGG terms. I was going to use clusterProfiler for this, but I can’t seem to get past constructing the gene list. I have followed the vignette…

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KEGG COMPOUND: C04020

KEGG COMPOUND: C04020     COMPOUND: C04020 Help Entry C04020                      Compound                                Name D-Lysopine;N2-(D-1-Carboxyethyl)-L-lysine;Lysopine Formula C9H18N2O4 Exact mass 218.1267 Mol weight 218.2502 Structure Mol fileKCF fileDB search Reaction Pathway Enzyme Other DBs KCF data Show ATOM        15            1   N1a N    25.5724  -27.5100            2   C1b C    26.7849  -28.2100            3   C1b C    27.9973  -27.5100            4   C1b C    29.2097  -28.2100            5   C1b C    30.4222  -27.5100            6   C1c C    31.6346  -28.2100            7   C6a C    32.8470  -27.5100            8   O6a O    34.0595  -28.2100            9   O6a O    32.8470  -26.1101            10  N1b N    31.6346  -30.1700            11  C1c C    30.4262  -30.8677            12  C6a C    29.2327  -30.1784            13  O6a O    28.0444  -30.8645            14  C1a C    30.4261  -32.2698            15  O6a O    29.2803  -29.0584BOND        14            1     1   2 1            2     2   3 1            3     3   4…

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Identification of Prognosis-Associated Biomarkers in Thyroid Carcinoma

Introduction Thyroid cancer (TC) is a common endocrine malignancy with a rapidly increasing incidence worldwide, and the estimated new cases and deaths are notably higher in women than in men.1 Papillary thyroid carcinoma (PTC) is identified as the most common pathological type of TC, and accounts for approximately 80–85% of…

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Classifiers for predicting coronary artery disease

Introduction Coronary artery disease (CAD) is a complex pathology associated with behavioral and environmental factors.1–3 CAD shows high prevalence and is associated with a high fatality rate among cardiovascular diseases. The main manifestations of CAD are stable or unstable angina pectoris and identifiable or unrecognized myocardial infarction.4 The main risk…

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High tumor mutation burden and DNA repair gene mutations

Introduction Anaplastic lymphoma kinase (ALK)‑fusion genes represent a small but important part of oncogenic driver mutations in NSCLC, accounting for approximately 3%‑7% of all cases worldwide.1,2 Small molecule tyrosine kinase inhibitors (TKIs) are the standard therapy for ALK-rearranged NSCLC. Crizotinib, a first-generation TKI, is the most widely used targeted drug…

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KEGG REACTION: R09076

Entry R09076                      Reaction                                Name spermidine:oxygen oxidoreductase (spermidine-forming) Definition Spermine + Oxygen + H2O <=> Spermidine + 3-Aminopropanal + Hydrogen peroxide Equation Reaction class Enzyme Pathway rn00330   Arginine and proline metabolism rn00770   Pantothenate and CoA biosynthesis rn01240   Biosynthesis of cofactors Module M00913   Pantothenate biosynthesis, 2-oxoisovalerate/spermine => pantothenate Orthology Other DBs Read more…

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Potter Clarkson and ERS Genomics to join forces with eureKARE on the eureKAWARDS

Potter Clarkson and ERS Genomics to join forces with eureKARE on the eureKAWARDS Potter Clarkson to offer the winner a Kick-StartiP consultancy ERS Genomics to provide the most promising CRISPR/Cas9 team with a complimentary three-year CRISPR/Cas9 license Luxembourg and Paris, France – 14 September 2021: eureKARE (“the Company”), a pioneering…

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KEGG REACTION: R00694

Entry R00694                      Reaction                                Name L-Phenylalanine:2-oxoglutarate aminotransferase Definition L-Phenylalanine + 2-Oxoglutarate <=> Phenylpyruvate + L-Glutamate Equation Reaction class RC00006   C00025_C00026  C00079_C00166 Enzyme Pathway rn00360   Phenylalanine metabolism rn00400   Phenylalanine, tyrosine and tryptophan biosynthesis rn00960   Tropane, piperidine and pyridine alkaloid biosynthesis rn01110   Biosynthesis of secondary metabolites rn01210   2-Oxocarboxylic acid metabolism rn01230   Biosynthesis of amino acids…

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KEGG ORTHOLOGY: K15816

Entry EC 4.2.1.128                Enzyme                                  Name lupan-3beta,20-diol synthase;LUP1 (gene name) Class Lyases;Carbon-oxygen lyases;Hydro-lyasesBRITE hierarchy Sysname (3S)-2,3-epoxy-2,3-dihydrosqualene hydro-lyase (lupan-3beta,20-diol-forming) Reaction(IUBMB) lupan-3beta,20-diol = (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O [RN:R09743] Reaction(KEGG) Substrate lupan-3beta,20-diol [CPD:C19863] Product (3S)-2,3-epoxy-2,3-dihydrosqualene [CPD:C01054]; H2O [CPD:C00001] Comment The reaction occurs in the reverse direction. The recombinant enzyme from Arabidopsis thaliana gives a 1:1 mixture of…

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Comparative genomics provides insights into the aquatic adaptations of mammals

Species invasions into novel habitats mark major transitions in the evolution of life on Earth. Some of these are relatively ancient, such as the vertebrate transition from the oceans to life on land (∼375 Mya) or the evolution of arboreal vertebrate species (∼160 Mya). When divergent lineages transition to the…

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Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

1. Hackstein JH, Stumm CK. Methane production in terrestrial arthropods. Proc Natl Acad Sci USA. 1994;91:5441–5. CAS  PubMed  PubMed Central  Article  Google Scholar  2. Hackstein JHP, van Alen TA. Fecal methanogens and vertebrate evolution. Evolution. 1996;50:559–72. PubMed  Article  PubMed Central  Google Scholar  3. Borrel G, McCann A, Deane J, Neto…

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KEGG REACTION: R08905

Entry RC00014                     RClass                                  Definition C5a-C6a:S2a+*-*+O6a:C1b+O5a-C1b+O6a Reactant pair Related class DB search Reaction Enzyme Pathway rn00020   Citrate cycle (TCA cycle) rn00072   Synthesis and degradation of ketone bodies rn00120   Primary bile acid biosynthesis rn00130   Ubiquinone and other terpenoid-quinone biosynthesis rn00280   Valine, leucine and isoleucine degradation rn00333   Prodigiosin biosynthesis rn00360   Phenylalanine metabolism rn00524   Neomycin,…

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Community detection protocol and failed gene enrichment

My data is a file of about 19000 genes from a 100 patients. I tried to use these data to create a network by using igraph. Firstly, I had all the names of the genes converted to ENTREZID and from the 19000 genes I kept around 14000. Then I had…

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kegg pathway database

Pathways that include all genes in gene_ids. Here the KEGG API operations are explained in comparison to these web tools. MODULE — modules or functional units of genes, BRITE — hierarchical classifications of biological entities, This page was last edited on 22 October 2020, at 18:43. The list can be…

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KEGG ENZYME: 1.14.12.17

Entry EC 1.14.12.17               Enzyme                                  Name nitric oxide dioxygenase Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donorBRITE hierarchy Sysname nitric oxide,NAD(P)H:oxygen oxidoreductase Reaction(IUBMB) 2 nitric oxide + 2 O2 + NAD(P)H =…

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Bioconductor – MetID

DOI: 10.18129/B9.bioc.MetID     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see MetID. Network-based prioritization of putative metabolite IDs Bioconductor version: 3.11 This package uses an innovative network-based approach that will enhance our ability to determine the identities of significant ions detected by…

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Gene expression profiling of contralateral dorsal root gangl

Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…

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copper c19520 in rok

CHAPTER 4 COPPER AND COPPER ALLOYS – PDF Free Download 80 196 Copper and Copper Alloys Table 43 Velocity Guidelines for Copper Alloys in Pumps and Propellers Operating in Seawater UNS Alloy Number Peripheral Velocity ft/s m/s C C C90300 C C95200 C C95500 C95700 C Source: Copper Development Association….

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Frontiers | DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)

Introduction Gene expression is not only controlled by DNA sequences but also by epigenetic marks in eukaryotes. DNA methylation as one of the important epigenetic modifications has been demonstrated as closely related to gene expression in biological processes, such as transcriptional activity, developmental regulation, and environmental responses (Maunakea et al.,…

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Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance

1. Lee, M.-R. et al. Mycobacterium abscessus complex infections in humans. Emerg. Infect. Dis. 21, 1638–1646 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Prince, D. S. et al. Infection with Mycobacterium avium complex in patients without predisposing conditions. N. Engl. J. Med. 321, 863–868 (1989). CAS  PubMed  Article  Google…

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KEGG COMPOUND: C00511

Entry C00511                      Compound                                Name Acrylic acid;Propenoate;Acrylate;2-Propenoic acid;Vinylformic acid Formula C3H4O2 Exact mass 72.0211 Mol weight 72.0627 Structure Mol fileKCF fileDB search Reaction Pathway map01120   Microbial metabolism in diverse environments map01220   Degradation of aromatic compounds Enzyme Other DBs KCF data Show ATOM        5            1   C6a C    25.5500  -16.7300            2   C2b C    26.7400  -17.4300            3   O6a O    25.5500  -15.3300            4   O6a O    24.3600  -17.4300            5   C2a C    28.0000  -16.7300BOND        4            1     1   2 1            2     1   3 1            3     1   4 2            4     2   5 2 Read…

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KEGG COMPOUND: C04751

KEGG COMPOUND: C04751     COMPOUND: C04751 Help Entry C04751                      Compound                                Name 1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate;1-(5′-Phosphoribosyl)-5-amino-4-imidazolecarboxylate;1-(5′-Phosphoribosyl)-5-amino-4-carboxyimidazole;5′-Phosphoribosyl-5-amino-4-imidazolecarboxylate;1-(5′-Phosphoribosyl)-4-carboxy-5-aminoimidazole;5′-Phosphoribosyl-4-carboxy-5-aminoimidazole;5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate Formula C9H14N3O9P Exact mass 339.0468 Mol weight 339.1959 Structure Mol fileKCF fileDB search Reaction Pathway map01110   Biosynthesis of secondary metabolites Module M00048   Inosine monophosphate biosynthesis, PRPP + glutamine => IMP Enzyme Other DBs KCF data Show ATOM        22            1   N4y N    19.7356  -16.9708            2   C1y C    18.7758  -18.1993            3   C8y…

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Psyt 502 error

Psyt 502 error 25-08-2021 PSYT Issues in Drug Dependence 3 Credits PSYT Brain Evolution & Psychiatry 3 Credits PSYT Advanced Studies in Addiction 3 Credits. Syntax Error. Usage: dbname:identifier. KEGG, ENZYME: , Help. Entry. EC Enzyme….

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How to compute module completion ratio of KEGG modules from KO identifiers? (command line)

How to compute module completion ratio of KEGG modules from KO identifiers? (command line) 0 I was previously using KEGG-MAPLE to compute module completion ratios for metagenome assembled genomes. However, this tool was web only (very frustrating) and also it has been discontinued. Now I’m trying to do something similar…

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Integrated bioinformatics analysis to identify abnormal CC

Introduction In recent years, the morbidity and mortality of colon cancer have increased rapidly, both being ranked fourth worldwide. Although surgery-based comprehensive treatments improve the prognosis of colon cancer, because of the lack of available means for early diagnosis, the mortality level remains high for patients with advanced-stage cancer. The…

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How to transform the deg gene list from seurat to a gene list input to clusterProfiler compareCluster ?

Sorry for lateness, I wanted to do something similar. This is what I did for reference: Using a Seurat generated gene list for input into ClusterProfiler to see the GO or KEGG terms per cluster. I’ll keep the meat and potatoes of the Seurat vignette in this tutorial: library(dplyr) library(Seurat)…

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issues installing pathfindR package

issues installing pathfindR package 1 Hi I am trying to use the pathfindR package to do enrichment analysis on my data. According to the vignette the package is downloaded from CRAN by install.packages(“pathfindR”) this gives the following output Installing package into �� (as �lib� is unspecified) Warning in install.packages :…

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UMAP of TRA/B

Hello, I have output from a single cell sequencing run that has both the VDJ and gene expression data. For the same cells, we also used a hybrid capture approach to sequence the TCR sequences. I have compared the TCR sequences across the two approaches and I have found a…

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How to merge the edited KEGG pathways in cytoscape

How to merge the edited KEGG pathways in cytoscape 1 I have learnt to import KEGG pathways to cytoscape and merge the pathways without any edits. but I want to differentiate the nodes of each pathways with different colours to understand the pathways of particular gene or molecule. when I…

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Sequence (annotation) databases in 2021

Forum:Sequence (annotation) databases in 2021 1 Hi everyone, So I know there are several threads on this topic already (or tangentially related to it). For example: But these threads are really old now. Things have probably changed quite significantly in the mean time. So I would like to start a…

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Bioinformatician — Biological data and network analysis

  EMBL is seeking to recruit a service Bioinformatician/data scientist at EMBL Heidelberg. The position is available in the group of Peer Bork, and will be integrated in the upcoming data science center at EMBL-Heidelberg from 2022 onwards. The successful candidate will be responsible for disseminating expertise, know-how, and guidance…

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KEGG COMPOUND: C02630

KEGG COMPOUND: C02630     COMPOUND: C02630 Help Entry C02630                      Compound                                Name 2-Hydroxyglutarate;alpha-Hydroxyglutarate Formula C5H8O5 Exact mass 148.0372 Mol weight 148.114 Structure Mol fileKCF fileDB search Reaction Pathway map00660   C5-Branched dibasic acid metabolism Enzyme Other DBs KCF data Show ATOM        10            1   C1c C    26.2500  -19.0400            2   C1b C    25.0600  -18.3400            3   C6a C    27.5100  -18.3400            4   O1a O    26.2500  -20.3700            5   C1b C    23.8000  -19.0400            6   O6a O    27.5100  -16.9400            7   O6a O    28.7000  -19.0400            8   C6a C    22.6100  -18.3400            9   O6a O    21.4200  -19.0400            10  O6a O    22.6100  -16.9400BOND        9            1     1   2 1            2     1   3 1            3     1   4…

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KEGG COMPOUND: C00499

KEGG COMPOUND: C00499     COMPOUND: C00499 Help Entry C00499                      Compound                                Name Allantoate;Allantoic acid Formula C4H8N4O4 Exact mass 176.0546 Mol weight 176.1307 Structure Mol fileKCF fileDB search Reaction Pathway map01120   Microbial metabolism in diverse environments Module M00546   Purine degradation, xanthine => urea Enzyme Other DBs KCF data Show ATOM        12            1   C1c C    26.9671  -25.7731            2   N1b N    25.3903  -26.4757            3   N1b N    28.4732  -26.4757            4   C6a…

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Limiting The Genes Associated With a Pathway to a Certain Species

Hello everyone! I am currently trying to establish a metabolic pathway analysis pipeline for my lab, using complete genomes. The final goal is to be able to see the primary metabolic pathways from a complete/draft genome. As a test, I am using the sequence of the complete genome of E….

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How to limit KAAS pathway results to certain species?

How to limit KAAS pathway results to certain species? 0 I’m working on a dataset in an insect species. I was using KAAS to annotate the genes. In the parameter for “GENES data set”, I only selected some species from insects. But in the results, the Pathway Mapping gave pathways…

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How can I add KEGG functional categories to whole genome alignments?

How can I add KEGG functional categories to whole genome alignments? 0 Hi! I am looking for packages/servers that can add KEGG gene functional categories to whole genome alignments done on ACT. A reference I am trying to emulate is in panel A here – www.nature.com/articles/nature06244/figures/2. How can I overlay…

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How to search for species with certain function or pathway in the annotated genome?

How to search for species with certain function or pathway in the annotated genome? 0 I’m trying to find bacterial species with certain metabolic pathways. I want to curate a “metagenome” of individual species that each have certain metabolic characteristics. So far, I have found KEGG has information on metabolic…

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How to colour points in cnetplot of clustprofiler?

I have a cnetplot from running enrichment with kegg using clusterprofiler. I have scores input as the fold change but for each gene in the plot they are not varying in colour to show their difference in the fold change score. My dataset is genes of entrez IDs and then…

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How to retrieve KO IDs for a list of genes?

How to retrieve KO IDs for a list of genes? 2 Hi, community!!! I have downloaded a list of genes from the MetaCyc database for some bacterial species. I want to find out their respective KO IDs. Can anyone please tell me how can I do that? Thanks KEGG database…

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KEGG pathway draw

KEGG pathway draw 0 hello, I would like to know the tool or software used for generating similar illustration: thank you for your help. KEGG transcriptome RNAseq • 17 views Login before adding your answer. Source link

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GSEA and over-representation analysis of many genes

GSEA and over-representation analysis of many genes 0 Hello everyone! I’ve been doing some Differential Expression analysis on specific samples. It happens that I found a lot of genes that are DE. In total, of 24000 features, 11000 were up or down regulated in control vs group. Even tough the…

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From EC terms to GO terms to GO enrichment

From EC terms to GO terms to GO enrichment 0 Hi I did a KEGG annotation of RNAseq data. I want do do GO enrichment next. I do have the EC numbers of the genes of interest, so I converted the EC numbers to GO terms using EC2GO. But I…

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What’s the difference between enrichKEGG and gseKEGG

What’s the difference between enrichKEGG and gseKEGG 3 Hi, I was wondering what is the difference between enrichKEGG and gseKEGG in R package ClusterProfile. Thanks! clusterprofiler KEGG • 2.3k views Source link

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Converting an S4 object into a dataframe in R

I have an S4 object named ‘res’ which I got while using an R package called RDAVIDWebService. I can’t seem to find a way to convert this object into a dataframe in R. I tried using the function ‘as.data.frame(res)’ but it throws this error: > as.data.frame(res) Error in as.data.frame.default(res) :…

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Converting an S4 object into a dataframe in R

I have an S4 object named ‘res’ which I got while using an R package called RDAVIDWebService. I can’t seem to find a way to convert this object into a dataframe in R. I tried using the function ‘as.data.frame(res)’ but it throws this error: > as.data.frame(res) Error in as.data.frame.default(res) :…

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Converting an S4 object into a dataframe in R

I have an S4 object named ‘res’ which I got while using an R package called RDAVIDWebService. I can’t seem to find a way to convert this object into a dataframe in R. I tried using the function ‘as.data.frame(res)’ but it throws this error: > as.data.frame(res) Error in as.data.frame.default(res) :…

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Converting an S4 object into a dataframe in R

I have an S4 object named ‘res’ which I got while using an R package called RDAVIDWebService. I can’t seem to find a way to convert this object into a dataframe in R. I tried using the function ‘as.data.frame(res)’ but it throws this error: > as.data.frame(res) Error in as.data.frame.default(res) :…

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Converting an S4 object into a dataframe in R

I have an S4 object named ‘res’ which I got while using an R package called RDAVIDWebService. I can’t seem to find a way to convert this object into a dataframe in R. I tried using the function ‘as.data.frame(res)’ but it throws this error: > as.data.frame(res) Error in as.data.frame.default(res) :…

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