cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12721611
title: Differential abundance and gene set enrichment in plasma of cancer patients versus controls

description: Version update: Human Protein Atlas v23 used for gene set enrichment analysis (instead of Human Protein Atlas v18)

DESeq2 differential abundance output for genes with q < 0.05 and |log2 fold change| > 1 in cancer vs control plasma samples:



differentialabundance_pancancer.txt: tables with differentially abundant genes (|log2(fold change)|>1 and adjusted p>0.05) per cancer-control comparison (cancertype) in a pan-cancer plasma sample cohort (25 locally advanced to metastatic cancer types - 7 or 8 patients per type - vs 8 cancer-free control donors)

differentialabundance_threecancer.txt: tables with differentially abundant genes (|log2(fold change)|>1 and adjusted p>0.05) per cancer-control comparison (cancertype) in the three-cancer plasma cohort (ovarian, prostate and uterine cancer - 11 or 12 patients per type - vs 20 cancer-free controls)



Gene_id: Ensembl gene id (GChr38 v91); baseMean: mean of normalized counts for all samples; log2FoldChange: log2 fold change for cancer vs control; lfcSE: standard error for cancer vs control; stat: Wald statistic for cancer vs control; pvalue: Wald test p-value for cancer vs control; padj: Benjamini-Hochberg corrected p-value; cancertype: respective cancer type abbreviation of cancer patient plasma samples that were compared to plasma samples of controls.




Gene set enrichment analyses based on fold change ranked gene lists (cancer versus control) - results obtained with fgea (v1.22.0):



customgenesets.txt: custom gene set lists based on RNA Atlas (&Human Protein Atlas), Tabula Sapiens, GTEX, TCGA data.



Reference: reference to create gene sets (including RNA Atlas, Human Protein Atlas, Tabula Sapiens, GTEX, and TCGA); set: set name; genes: gene list for set



GSEA_pancancer.txt & GSEA_threecancer.txt: gene set enrichment results based on fold change ranked gene list (specific cancer type versus controls) in pan-cancer cohort and three-cancer cohort, respectively



Sets: gene set category (HALLMARK and KEGG: Hallmark and Canonical Pathways gene sets obtained from MSigDB (v2022.1); CUSTOM: custom tissue and cell type specific gene sets as defined in customgenesets.txt); pathway: pathway/set name; pval: enrichment p-value; padj: Benjamini-Hochberg adjusted p-value; log2err: expected error for the standard deviation of the P-value logarithm; ES: enrichment score, same as in Broad GSEA implementation; NES: enrichment score normalized to mean enrichment of random samples of the same size; size: size of the pathway after removing genes without statistic values; leadingEdge: leading edge genes that drive the enrichment; Disease: respective cancer type abbreviation of cancer patient plasma samples that were compared to plasma samples of controls
DOI: 10.5281/zenodo.7953707
title: Differential abundance and gene set enrichment in plasma of cancer patients versus controls

description: Version update: Human Protein Atlas v23 used for gene set enrichment analysis (instead of Human Protein Atlas v18)

DESeq2 differential abundance output for genes with q < 0.05 and |log2 fold change| > 1 in cancer vs control plasma samples:



differentialabundance_pancancer.txt: tables with differentially abundant genes (|log2(fold change)|>1 and adjusted p>0.05) per cancer-control comparison (cancertype) in a pan-cancer plasma sample cohort (25 locally advanced to metastatic cancer types - 7 or 8 patients per type - vs 8 cancer-free control donors)

differentialabundance_threecancer.txt: tables with differentially abundant genes (|log2(fold change)|>1 and adjusted p>0.05) per cancer-control comparison (cancertype) in the three-cancer plasma cohort (ovarian, prostate and uterine cancer - 11 or 12 patients per type - vs 20 cancer-free controls)



Gene_id: Ensembl gene id (GChr38 v91); baseMean: mean of normalized counts for all samples; log2FoldChange: log2 fold change for cancer vs control; lfcSE: standard error for cancer vs control; stat: Wald statistic for cancer vs control; pvalue: Wald test p-value for cancer vs control; padj: Benjamini-Hochberg corrected p-value; cancertype: respective cancer type abbreviation of cancer patient plasma samples that were compared to plasma samples of controls.




Gene set enrichment analyses based on fold change ranked gene lists (cancer versus control) - results obtained with fgea (v1.22.0):



customgenesets.txt: custom gene set lists based on RNA Atlas (&Human Protein Atlas), Tabula Sapiens, GTEX, TCGA data.



Reference: reference to create gene sets (including RNA Atlas, Human Protein Atlas, Tabula Sapiens, GTEX, and TCGA); set: set name; genes: gene list for set



GSEA_pancancer.txt & GSEA_threecancer.txt: gene set enrichment results based on fold change ranked gene list (specific cancer type versus controls) in pan-cancer cohort and three-cancer cohort, respectively



Sets: gene set category (HALLMARK and KEGG: Hallmark and Canonical Pathways gene sets obtained from MSigDB (v2022.1); CUSTOM: custom tissue and cell type specific gene sets as defined in customgenesets.txt); pathway: pathway/set name; pval: enrichment p-value; padj: Benjamini-Hochberg adjusted p-value; log2err: expected error for the standard deviation of the P-value logarithm; ES: enrichment score, same as in Broad GSEA implementation; NES: enrichment score normalized to mean enrichment of random samples of the same size; size: size of the pathway after removing genes without statistic values; leadingEdge: leading edge genes that drive the enrichment; Disease: respective cancer type abbreviation of cancer patient plasma samples that were compared to plasma samples of controls
DOI: 10.5281/zenodo.7953708
title: Differential abundance and gene set enrichment in plasma of cancer patients versus controls

description: DESeq2 differential abundance output for genes with q &lt; 0.05 and |log<sub>2</sub> fold change| &gt; 1 in cancer vs control plasma samples: <em>differentialabundance_pancancer.txt</em>: tables with differentially abundant genes (|log2(fold change)|&gt;1 and adjusted p&gt;0.05) per cancer-control comparison (cancertype) in a pan-cancer plasma sample cohort (25 locally advanced to metastatic cancer types - 7 or 8 patients per type - vs 8 cancer-free control donors) <em>differentialabundance_threecancer.txt</em>: tables with differentially abundant genes (|log2(fold change)|&gt;1 and adjusted p&gt;0.05) per cancer-control comparison (cancertype) in the three-cancer plasma cohort (ovarian, prostate and uterine cancer - 11 or 12 patients per type - vs 20 cancer-free controls) Gene_id: Ensembl gene id (GChr38 v91); baseMean: mean of normalized counts for all samples; log2FoldChange: log2 fold change for cancer vs control; lfcSE: standard error for cancer vs control; stat: Wald statistic for cancer vs control; pvalue: Wald test p-value for cancer vs control; padj: Benjamini-Hochberg corrected p-value; cancertype: respective cancer type abbreviation of cancer patient plasma samples that were compared to plasma samples of controls. Gene set enrichment analyses based on fold change ranked gene lists (cancer versus control) - results obtained with fgea (v1.22.0): <em>customgenesets.txt</em>: custom gene set lists based on RNA Atlas (&Human Protein Atlas), Tabula Sapiens, GTEX, TCGA data. Reference: reference to create gene sets (including RNA Atlas, Human Protein Atlas, Tabula Sapiens, GTEX, and TCGA); set: set name; genes: gene list for set <em>GSEA_pancancer.txt</em> & <em>GSEA_threecancer.txt</em>: gene set enrichment results based on fold change ranked gene list (specific cancer type versus controls) in pan-cancer cohort and three-cancer cohort, respectively Sets: gene set category (HALLMARK and KEGG: Hallmark and Canonical Pathways gene sets obtained from MSigDB (v2022.1); CUSTOM: custom tissue and cell type specific gene sets as defined in <em>customgenesets.txt)</em>; pathway: pathway/set name; pval: enrichment p-value; padj: Benjamini-Hochberg adjusted p-value; log2err: expected error for the standard deviation of the P-value logarithm; ES: enrichment score, same as in Broad GSEA implementation; NES: enrichment score normalized to mean enrichment of random samples of the same size; size: size of the pathway after removing genes without statistic values; leadingEdge: leading edge genes that drive the enrichment; Disease: respective cancer type abbreviation of cancer patient plasma samples that were compared to plasma samples of controls
DOI: 10.15468/dl.x6n63a
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (EN, VU)",
 "OccurrenceStatus is Present",
 "TaxonKey is Ophiocordyceps sinensis (Berk.) G.H.Sung, J.M.Sung, Hywel-Jones & Spatafora"
 ]
}

 The dataset includes 126 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020429-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d9y4s2
title: Occurrence Download

description: A dataset containing 7233 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Solidago uliginosa Nutt., Solidago uliginosa var. linoides (Torr. & A.Gray) Fernald, Solidago uliginosa var. neglecta (Torr. & A.Gray) Fernald, Solidago uliginosa var. levipes (Fernald) Fernald)"
 ]
}

 The dataset includes 7233 records from 155 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020430-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12598884
title: SCORE D3.9 - Models for the long-term evolution of the coastline (package)

description: SCORE project TD3.9 datasets and scripts:

Modelling tools and local datasets produced in the SCORE Task 3.5, for the long-term evolution of the coastline and uncertainties, estimated by the study of local morphodynamic processes and climatic projections. It contains a hybrid 2D/3D modelling chain, for sediment transport processes connected to hydrodynamic models at the storm scale.
DOI: 10.5281/zenodo.12598885
title: SCORE D3.9 - Models for the long-term evolution of the coastline (package)

description: SCORE project TD3.9 datasets and scripts:

Modelling tools and local datasets produced in the SCORE Task 3.5, for the long-term evolution of the coastline and uncertainties, estimated by the study of local morphodynamic processes and climatic projections. It contains a hybrid 2D/3D modelling chain, for sediment transport processes connected to hydrodynamic models at the storm scale.
DOI: 10.15468/dl.2hysrg
title: Occurrence Download

description: A dataset containing 2328 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Acacia calamifolia Sweet ex Lindl."
 ]
}

 The dataset includes 2328 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020431-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dyf78c
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Solidago uliginosa var. terrae-novae (Torr. & A.Gray) Fernald"
 ]
}

 The dataset includes 19 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020433-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4w95m5
title: Occurrence Download

description: A dataset containing 235 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-96.86065 -18.6641,-32.5301 -18.6641,-32.5301 19.18174,-96.86065 19.18174,-96.86065 -18.6641))",
 "TaxonKey is one of (Sarcomphalus cinnamomum (Triana & Planch.) Hauenschild, Ziziphus itacaiunensis Fróes)"
 ]
}

 The dataset includes 235 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020434-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fe4ncp
title: Occurrence Download

description: A dataset containing 25013 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Specimen, Living Specimen, Occurrence evidence)",
 "Continent is Europe",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is one of (Coordinate rounded, Geodetic datum assumed WGS84, Coordinate reprojected, Coordinate precision invalid, Coordinate uncertainty meters invalid, Coordinate precision/uncertainty mismatch, Country derived from coordinates, Continent derived from country, Continent derived from coordinates, Presumed swapped coordinate, The scientific name ID was not used in backbone matching, The taxon concept ID was not used in backbone matching, The taxon ID was not used in backbone matching, The scientific name ID was not found in the checklist, The taxon concept ID was not found in the checklist, The taxon ID was not found in the checklist, Depth min max swapped, Elevation min max swapped, Multimedia date invalid, Multimedia URI invalid, Occurrence status inferred from individual count, ccurrence status inferred from basis of record)",
 "TaxonKey is Lynx lynx (Linnaeus, 1758)",
 "Year 2014-2024"
 ]
}

 The dataset includes 25013 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020432-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.99cwqv
title: Occurrence Download

description: A dataset containing 512480 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "Geometry POLYGON((118 35,136 35,136 60,118 60,118 35))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 1980-2024"
 ]
}

 The dataset includes 512480 records from 319 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020419-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4u2f9u
title: Occurrence Download

description: A dataset containing 225 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Asemeia ovata (Poir.) J.F.B.Pastore & J.R.Abbott"
 ]
}

 The dataset includes 225 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069799-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.474yan
title: Occurrence Download

description: A dataset containing 1016 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gastrotheca riobambae (Fowler, 1913)"
 ]
}

 The dataset includes 1016 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0099224-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8m3us4
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Palicourea carnosocarpa (Dwyer & M.V.Hayden) C.M.Taylor"
 ]
}

 The dataset includes 9 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0177819-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ev87h5
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriocaulon araguaiense A.L.R.Oliveira & C.P.Bove"
 ]
}

 The dataset includes 9 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0200730-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ra776w
title: Occurrence Download

description: A dataset containing 304 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rostrhamus sociabilis plumbeus Ridgway, 1874"
 ]
}

 The dataset includes 304 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069806-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fypn57
title: Occurrence Download

description: A dataset containing 1016 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gastrotheca riobambae (Fowler, 1913)"
 ]
}

 The dataset includes 1016 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0099225-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6jrtnq
title: Occurrence Download

description: A dataset containing 1275 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriocaulon miquelianum Körn."
 ]
}

 The dataset includes 1275 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0200742-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.juvh3h
title: Occurrence Download

description: A dataset containing 296 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Living Specimen"
 ]
 },
 "Country is Mexico",
 "HasCoordinate is true",
 "TaxonKey is Acalypha diversifolia Jacq.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 296 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069810-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qykiqm
title: Occurrence Download

description: A dataset containing 1016 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gastrotheca riobambae (Fowler, 1913)"
 ]
}

 The dataset includes 1016 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0099227-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.adsu8h
title: Occurrence Download

description: A dataset containing 13043 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mesodon Férussac, 1821"
 ]
}

 The dataset includes 13043 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069810-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q9bk9g
title: Occurrence Download

description: A dataset containing 315 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriocaulon depressum R.Br. ex Sm."
 ]
}

 The dataset includes 315 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0200735-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nappbd
title: Occurrence Download

description: A dataset containing 1016 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gastrotheca riobambae (Fowler, 1913)"
 ]
}

 The dataset includes 1016 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0099229-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.57xjf3
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nolana chancoana M.O.Dillon & Quip."
 ]
}

 The dataset includes 33 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0177820-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m75fkb
title: Occurrence Download

description: A dataset containing 64 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriocaulon australasicum (F.Muell.) Körn."
 ]
}

 The dataset includes 64 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0200746-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.papacx
title: Occurrence Download

description: A dataset containing 10289 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-91.34033 34.70549,-81.67236 34.70549,-81.67236 37.0201,-91.34033 37.0201,-91.34033 34.70549))",
 "HasGeospatialIssue is false",
 "TaxonKey is Lanius ludovicianus Linnaeus, 1766"
 ]
}

 The dataset includes 10289 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069812-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.41hruy
title: Occurrence Download

description: A dataset containing 181 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Dominican Republic",
 "TaxonKey is Polystichum Roth"
 ]
}

 The dataset includes 181 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006359-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xygz1u
title: Occurrence Download

description: A dataset containing 1016 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gastrotheca riobambae (Fowler, 1913)"
 ]
}

 The dataset includes 1016 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0099230-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.csj3sd
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pteroclididae",
 "Continent is one of (North America, South America)"
 ]
}

 The dataset includes 5 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061798-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.