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3421 Data files visible to you, out of a total of 5622

Data file for PLaSMo accesssion ID PLM_1045, version 1

Concentrations of PFAS in liver and PAH metabolites in bile of cod exposed to mixtures of PAHs and PFASs

Creator: Karina Dale

Submitter: Karina Dale

Measurements of PAH metabolites in bile in fish caged in Kollevåg.

Creator: Karina Dale

Submitter: Karina Dale

We constructed a logic-based model to unravel mechanisms underlying pancreatic cancer and fibrosis. Model was calibrated with expression data and simulated for stimulus response and perturbation analysis to identify disease markers. Disease markers predicted by the model are validated through patient data using KM survival plot (which stratify patient into short and long survival) and box plot (expression level of the markers in normal vs. pancreatic patients). In vitro validations of the model ...

Contains training data and model with addition of the NoxE reaction 6h, 24h and 48h metabolite concentration data as well as calculated oxygen concentrations assuming no diffusion limit through the biofilm layer

Data file for PLaSMo accesssion ID PLM_42, version 1

Creators: BioData SynthSys, Jonathan Massheder

Submitter: BioData SynthSys

Contains the estimated oxygen concentration and metabolite concentrations as wel as the model with addition of an oxygen inhibition parameter. Results: Addition of the oxygen inhibition term does not improve the modell with the current parameter set

Data file for PLaSMo accesssion ID PLM_2, version 1

Data file for PLaSMo accesssion ID PLM_24, version 1

Creators: BioData SynthSys, Jonathan Massheder

Submitter: BioData SynthSys

Batch sample publishing

Batch sample publishing

Batch sample publishing

No description specified
No description specified

Description of PCR validation results expressed as 2 -ΔΔCt of miR 25-3p, miR 185-5p and miR 132-3p

Creator: Gabriela Loscalzo

Submitter: Gabriela Loscalzo

Description of PCR validation results expressed as 2 -ΔΔCt of miR 25-3p, miR 185-5p and miR 132-3p

Creator: Gabriela Loscalzo

Submitter: Gabriela Loscalzo

Description of PCR validation results expressed as 2 -ΔΔCt of miR 25-3p, miR 185-5p and miR 132-3p

Creator: Gabriela Loscalzo

Submitter: Gabriela Loscalzo

Zip-archive with induced fit docking results for reference compounds methotrexate and 1b as well as the N10-modified compounds 2a and 2e in their neutral and N1-protonated variants and the N10-modified compound 2c and merged-series compound 5e in neutral form as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The TbPTR1 receptor was based on PDB-ID 2x9g with explicit conserved structural water molecules. Docking results were obtained by Induced ...

Zip-archive with induced fit docking results for reference compounds methotrexate, 1b and 1c as well as the N10-modified compound 2e in their neutral and N1-protonated variants and the PABA-modified compound 3e in neutral form as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The LmPTR1 receptor was based on PDB-ID 1e92 with explicit conserved structural water molecules. Docking results were obtained by Induced Fit docking with Schrödinger ...

Zip-archive with induced fit docking results for reference compounds methotrexate and 1b as well as the N10-modified compounds 2a and 2e in their neutral and N1-protonated variants and the PABA-modified compound 3d in neutral form as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The TbPTR1 receptor was based on PDB-ID 2x9g without additional water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and ...

Zip-archive with induced fit docking results for reference compounds methotrexate, 1b and 1c as well as the N10-modified compound 2e in their neutral and N1-protonated variants and the N10-modified compound 2a and Tail-modified compounds 4e, 4f, 4i and 4j in neutral form as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The LmPTR1 receptor was based on PDB-ID 1e92 without additional water molecules. Docking results were obtained by Induced ...

Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The hDHFR receptor was based on PDB-ID 1u72 with explicit conserved structural water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Induced ...

Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The hDHFR receptor was based on PDB-ID 1u72 without additional water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Induced Fit Docking ...

Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The LmDHFR receptor was based on a published homology model of LmDHFR (Panecka-Hofman et al. (2017) Biochim Biophys Acta Gen Subj. 1861(12), 3215-3230. DOI: 10.1016/j.bbagen.2017.09.012) without additional water molecules. Docking results were obtained by Induced Fit docking with Schrödinger ...

Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The TbDHFR receptor was based on PDB-ID 3rg9 without additional water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Induced Fit Docking ...

Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the hDHFR receptor based on PDB-ID 1u72 with explicit conserved structural water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file. ...

Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the hDHFR receptor based on PDB-ID 1u72 without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file.

Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the LmDHFR receptor based on the published homology model of LmDHFR (Panecka-Hofman et al. (2017) Biochim Biophys Acta Gen Subj. 1861(12), 3215-3230. DOI: 10.1016/j.bbagen.2017.09.012) without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, ...

Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the LmPTR1 receptor based on PDB-ID 1e92 with explicit conserved structural water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file. ...

Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the LmPTR1 receptor based on PDB-ID 1e92 without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file.

Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the TbDHFR receptor based on PDB-ID 3rg9 without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file.

Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the TbPTR1 receptor based on PDB-ID 2x9g with explicit conserved structural water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file. ...

Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the TbPTR1 receptor based on PDB-ID 2x9g without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file.

Data file for PLaSMo accesssion ID PLM_11, version 2

Linked with model: 10.15490/fairdomhub.1.model.802.1

Creators: None

Submitter: James Wordsworth

Linked with Model: 10.15490/fairdomhub.1.model.802.1

Creators: None

Submitter: James Wordsworth

Linked with model: 10.15490/fairdomhub.1.model.802.1

Creators: None

Submitter: James Wordsworth

Filtering of data in Perseus and t-test between conditions Perseus save file

A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling. The publication for the introduction and analysis of the benchmark problem collection is available at https://academic.oup.com/bioinformatics/article/35/17/3073/5280731.

Creators: Wolfgang Müller, Jan Hasenauer, Leonard Schmiester, PETab team and INCOME Hackathon Hackers

Submitter: Wolfgang Müller

Experimental data set for the kinetic characterisation of PFK

Experimental data set for the kinetic characterisation of PGI

Kinetic characterisation of PGK. Expermental data for enzyme reaction rates with increasing concentrations of ATP, ADP, BPG and 3PG.

Experimental data set for the kinetic characterisation of PGK

Simulation results of PGK experimental data for ADP, ATP, 3PG and BPG saturation.

PGK yeast with recycling of ATP

PGK yeast without recycling of ATP

incubations with yeast enzymes at 30C

No description specified
No description specified

Experimental data for the phosphoglycerate mutase (EC 5.4.2.12) activity.

_p_RNAinVAL/_I_01_LabTrials/

Creator: Marko Petek

Submitter: Marko Petek

_p_RNAinVAL/_I_01_LabTrials/

Creator: Marko Petek

Submitter: Marko Petek

_p_RNAinVAL/_I_03_Omics/

Creator: Marko Petek

Submitter: Marko Petek

_p_RNAinVAL/_I_01_LabTrials/_S_05_jun2016/_A_01_jun2016-phenotyping/

Creator: Marko Petek

Submitter: Marko Petek

_p_SUSPHIRE/_I_T21_SXPsysbio/

Creator: Marko Petek

Submitter: Marko Petek

Phosphorylation site of the HPr protein detected ba mass spectromety

Creators: Michael Hecker, Joerg Stuelke

Submitter: Leif Steil

Data for the photometric determination of the activity for the under study enzymes.

Creator: Eleni Konia

Submitter: Ioannis Metaxas

Experimental data set for the kinetic characterisation of PK

Levels of cortisol+total protein and activities of cholinesterase, alanine aminotransferase (ALAT) and aspartate aminotransferase (ASAT) in plasma of cod exposed to chlorpyrifos-methyl

Creators: Karina Dale, Pål A. Olsvik

Submitter: Karina Dale

PMA1

Creator: Paul Heusden

Submitter: The JERM Harvester

Data file for PLaSMo accesssion ID PLM_1045, version 1

Liver samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.

Muscle samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.

Salmon feed switch experiment: Lipidomic data (POS mode) of gut tissue samples.

Salmon feed switch experiment: Lipidomics data (POS mode) of liver samples.

Salmon feed switch experiment: Lipidomic data (POS mode) of muscle tissue samples.

Salmon feed experiment: Lipidomic data (POS mode) of liver samples from fresh water sampling.

Salmon feed experiment: Lipidomic data (POS mode) of muscle samples from fresh water sampling.

Positive mode metabolomics of the same muscle tissue sample at multiple levels of dilution.

Samples of 40 45 50 55 60 mg were diluted in the same volume, then analysed. The resulting data describe the same tissue at different levels of dilution. From this we can devise some numerical post-processing that would make all samples "similar" based on the mass of tissue. This post-processing could then be applied to later samples given their mass.

NOTE: Sample does not come from the salmon feed-switch ...

Positive mode metabolomics of liver samples from saltwater sampling.

Positive mode metabolomics of muscle samples from saltwater sampling.

Complete posterior distributions for each drug and condition.

The files are in the hdf5 format and contain the complete information of the analysis for a FAIR data sharing.

Creators: None

Submitter: Sebastian Höpfl

The Results of the analysis are structured in three parts:

  1. The results of the main analysis
  2. The results with a broader prior (Sensitivity analysis)
  3. The Results of the multiple period comparison

For each part, full posterior traces for all analysis and visualizations of the paper are avalable.

Furthermore the diagnostics and traces were added for the different analysis. The trace for the mulitple comparison was to large to upload it and is available on request.

TRK1, TRK2

Creator: Silvia Petrezselyova

Submitter: The JERM Harvester

PPZ1

Creator: Paul Heusden

Submitter: The JERM Harvester

Source code is at https://gitlab.com/digisal/GSF1_metabolomics/. The report loads smoothly in Chrome, but is very slow to load in Firefox.

overview of sysmo-LAB2

Creator: Bas Teusink

Submitter: Bas Teusink

No description specified

Creator: Margrete Solheim

Submitter: Margrete Solheim

No description specified

Creator: Margrete Solheim

Submitter: Margrete Solheim

No description specified

Creator: Margrete Solheim

Submitter: Margrete Solheim

Mean values of clock gene RNA data in absolute units of RNA copies per cell (calculated from copies per gFW, / 25 million cells/gFW) from TiMet WP1.1, RNA dataset ros (from rosettes). Note the Col data are from WP1.1, not substituted with Col from the LD12:12 of the WP1.2 photoperiod data set, as they were in Flis et al. 2015. Note also that cL_m in these data is taken from CCA1 only, not the average of CCA1 and LHY as in the data sets used for optimisation of P2011.2.1 in Flis et al. 2015.

The ...

SD values of clock gene RNA data in absolute units of RNA copies per cell (calculated from copies per gFW, / 25 million cells/gFW) from TiMet WP1.1, RNA dataset ros (from rosettes). Note the Col data are from WP1.1, not substituted with Col from the LD12:12 of the WP1.2 photoperiod data set, as they were in Flis et al. 2015. Note also that cL_m in these data is taken from CCA1 only, not the average of CCA1 and LHY as in the data sets used for optimisation of P2011.2.1 in Flis et al. 2015.

The ...

No description specified

Including 294 genes and 1222 Breast cancer Patient. This is an input data for WGCNA

Including 277 genes and 1222 Breast cancer patients. This is an input data for WGCNA.

Including 289 genes and 1222 Breast cancer patient This is an input data for WGCNA

Including 91 genes and 1222 Breast cancer patient This is an input data for WGCNA

Data files for the conversion of XYL to KG, via the sequential addition of the Caulobacter crescentus Weimberg pathway enzymes, XDH, XLA, XAD, KDXD, KGSADH.

  • Summary of nuclear proteins
  • Separate sheets of nuclear processes (MBNP_Histones, DNA replication, DNA repair, RNA processing (rRNA and mRNA processing), transcription, import and export, ubiquitylation, proteasome, biogenesis ribosomes)
  • Ribosomes (category translation)

Tab color: Summary, purple; nuclear processes, green; ribosomes, orange

Creators: None

Submitter: Jana Kalvelage

Relative protein expression of the proteins Cyp3a and Mt in cod from the Kollevåg study

Creators: None

Submitter: Karina Dale

No description specified

Data file containing protein ID and pre-processed proteomic data, in addition to protein groups (peptide counts etc) determined in cod liver of cod exposed to PAH and PFAS mixtures.

Creator: Karina Dale

Submitter: Karina Dale

No description specified

Creator: Joerg Stuelke

Submitter: Leif Steil

List of protein identified proteins in SPINE experiment.

Creators: Joerg Stuelke, Uwe Voelker

Submitter: Leif Steil

Representation of all prepared 2D PAGE analyses of cytosolic proteins of Clostridium acetobutylicum growing continuously at pH 5.5, 5.3, 5.1, 4.9 and 4.7.

All spots and identified proteins of Clostridium acetobutylicum growing at steady-state pH 5.7 (acidogenesis) and pH 4.5 (solventogenesis), respectively, using 2D PAGE and Maldi-TOF analysis. The focus were cytosolic proteins with an isoelectric point bewteen 4 and 7 as well as a molecular weight of 180-10 kDa.

Maxquant output.

Proteomics data comparing LXX cultures cultivated on mineral and in continuous culture: mineral samples: LNU-LXX9-Si00-14B-P-B-Pr LNU-LXX9-Si00-14B-P-C-Pr LNU-LXX9-Si00-14B-P-D-Pr conitnuous culture samples: LNU-LXX9-Si00-CnA-P-B2-Pr LNU-LXX9-Si00-CnA-P-B3-Pr LNU-LXX9-Si00-CnA-P-B4-Pr LNU-LXX9-Si00-CnA-P-B5-Pr LNU-LXX9-Si00-CnA-P-B6-Pr LNU-LXX9-Si00-CnA-P-B7-Pr

Data curation notes provided by Alex Graf via Willi Gruissem, in addition to the PRIDE deposition.

The Excel file gives the list of samples uploaded into PRIDE. here - https://fairdomhub.org/data_files/3704

The published experimental design might lead one to expect 4x3x2x7 = 168 samples. There are more than 168 samples in the PRIDE upload for the following reasons:

First, all of the measurements from the experiment had been uploaded, including files for measurements that were repeated because of ...

This template is a JERM compliant spreadsheet for use with gel electrophoresis data. It is in the style of the JERM MASTER template with worksheets for metadata, organism_sample, instrument and data. To conform to MIAPE-GE all worksheets are mandatory. A detailed description of MIAPE-GE is available from http://www.psidev.info/miape/MIAPE_GE_1_4.pdf

Comparative proteomics of S. solfatricus grown on either L-fucose or D-glucose.

This is an Excel template for Mass Spec data that contains all the necessary MIAPE metadata fields. It was derived from examples on the PRIDE website (PRoteomics IDEntifications database http://www.ebi.ac.uk/pride/)

An example of a blank data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of MIAPE compliant data.

The shreadsheet contains macros to help you annotate your data with terms from controlled vocabularies and ontologies

An example of a completed data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of a MIAPE compliant data format taken from the PRIDE website (http://www.ebi.ac.uk/pride).

These files contain the output results from Phenyx searching, providing all necessary information for matching MS data with protein database.

This file contains the results from proteome analysis of Sulfolobus solfataricus grown on Caseinhydrolysate as carbon source (growth on D-glucose served as reference condition).

Protein copy number estimates, Mean and SD based on multiple proteomics experiments. Compatible with internal and external metabolite measurements for Growth curve A. Used as training data for the model

The causal interactions service provides the extracted data of causality from Reactome database.

Shared version of Publication "Welcome to the Family: Identification of the NAD+ Transporter of Animal Mitochondria as Member of the Solute Carrier Family SLC25"

Creators: Mathias Ziegler, Ines Heiland, Magnus Monné, Andrey Nikiforov, Gennaro Agrimi, Ferdinando Palmieri

Submitter: Olga Krebs

This document outlines our plans for making it easier to publish assets from SEEK to enable people from outside the consortium to see them.

Creator: Katy Wolstencroft

Submitter: Katy Wolstencroft

Data file for the Pyridoxamine phosphate formation assay

Creator: Eleni Konia

Submitter: Ioannis Metaxas

No description specified

Zip file with Python module used to correlate compound descriptors predicted with Schroedinger QikProp with observed anti-parasitic effect against T. brucei brucei bloodstream forms. The script allows a leave-one-out analysis in addition to the default correlation analysis, where data for each compound is skipped once before the correlation analysis is re-performed. An example config file is provided with the zip-archive. For further instructions and information on the available settings, also ...

Zip-file with Python module used to calculate trivariate statistics between the inhibition of parasitic target enzymes pteridine reductase 1 and dihydrofolate reductase and the corresponding inhibition of T. brucei brucei bloodstream forms. The script makes use of an expansion of pairwise Pearson or Spearman correlations. For further details, also refer to the README file.

A collection of python scripts used to generate CML from csv (CSV_to_CML.py), apply machine learning (Gradient Boosting using decision trees, prediction_viscosity.py), model based on eq 6 in the associated publication, and to plot the generated data (plot*.py).

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