Data files

Statistics of GO and GOA from Jan 2015 to Dec 2021

Created: 8th Apr 2024 at 21:11

The evolution of Gene Ontology

The table shows the number of terms, annotations and edges from Jan 2015 to Dec 2021.

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Exploring the Evolution of the Gene Ontology an...

Studies: Exploring how the concept and structure was inf...

Top20 nodes with highest Degree Centrality score

Created: 8th Apr 2024 at 21:09

The evolution of Gene Ontology

The table shows the top 20 nodes with the highest degree centrality score in BP, MF and CC

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Exploring the Evolution of the Gene Ontology an...

Studies: Exploring how the concept and structure was inf...

Reviewed and unreviewed proteins

Created: 8th Apr 2024 at 21:02

The evolution of Gene Ontology

Downloaded from UniprotKB

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Exploring the Evolution of the Gene Ontology an...

Studies: Exploring how the concept and structure was inf...

Supplementary file 2: Publications surveyed

Created: 8th Apr 2024 at 20:55

FAIR Functional Enrichment

This file provides a full list of the PubMed IDs used as input to our survey of SARS-CoV2 enrichment analysis results

Creators: None

Submitter: Yi Chen

Investigations: FAIR Functional Enrichment: Assessing and Model...

Studies: FAIR Functional Enrichment

Assays: FAIR Functional Enrichment

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Created: 28th Nov 2022 at 13:05, Last updated: 13th Jan 2023 at 08:33

Supplementary file 1: Search Terms

FAIR Functional Enrichment

A list of the search terms used for identifying SARS-CoV2 studies involving enrichment analysis. A random sample of 100 papers were used as input to the experiment.

Creators: None

Submitter: Yi Chen

Investigations: FAIR Functional Enrichment: Assessing and Model...

Studies: FAIR Functional Enrichment

Assays: FAIR Functional Enrichment

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Created: 28th Nov 2022 at 13:04, Last updated: 13th Jan 2023 at 08:31

FPKM value of breast cancer patient

Consensus Hallmark Annotation

1222 patients

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

prognostic genes of 17 cancer types

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Created: 5th Mar 2021 at 17:57, Last updated: 5th Mar 2021 at 17:57

Consensus Hallmark Annotation

No description specified

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Gene enrichment analysis output of modules

Assays: Jaccard Index Prognostic Hallmark Genes

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Created: 5th Mar 2021 at 10:05, Last updated: 5th Mar 2021 at 10:05

Consensus Hallmark Annotation

For each module, GSEA analysis was conducted by using web-tool g:profiler and only biological process (BP) were retained. Parameters for GSEA are default.

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Assays: Hub genes of modules and enriched GO terms

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Created: 7th Feb 2021 at 23:42, Last updated: 9th Feb 2021 at 10:42

Consensus Hallmark Annotation

Calculated by using R package GOSemSim.

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Assays: Hub genes of modules and enriched GO terms

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Created: 7th Feb 2021 at 23:53, Last updated: 9th Feb 2021 at 10:42

Modules and hub genes

Consensus Hallmark Annotation

Modules were identified by WGCNA. hub genes of each modules were identified based on intramodular degree.

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Abbreviations of 17 cancer types

Assays: Hub genes of modules and enriched GO terms

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Created: 7th Feb 2021 at 23:37, Last updated: 9th Feb 2021 at 10:42

Consensus Hallmark Annotation

No description specified

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Assays: Jaccard Index Prognostic Hallmark Genes

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Created: 7th Feb 2021 at 23:48, Last updated: 9th Feb 2021 at 10:42

Jaccard index score

Consensus Hallmark Annotation

No description specified

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Prognostic-hallmark genes of GO4 with log transformed FPKM value

Assays: Jaccard Index Prognostic Hallmark Genes

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Created: 3rd Feb 2021 at 18:39, Last updated: 9th Feb 2021 at 10:40

Consensus Hallmark Annotation

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

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Prognostic-hallmark genes of GO3 with log transformed FPKM value

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Created: 3rd Feb 2021 at 15:54, Last updated: 9th Feb 2021 at 10:40

Consensus Hallmark Annotation

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

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Prognostic-hallmark genes of GO2 with log transformed FPKM value

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Created: 3rd Feb 2021 at 15:52, Last updated: 9th Feb 2021 at 10:38

Consensus Hallmark Annotation

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

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Prognostic-hallmark genes of GO1 with log transformed FPKM value

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Created: 3rd Feb 2021 at 15:51, Last updated: 9th Feb 2021 at 10:37

Consensus Hallmark Annotation

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

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Download

Created: 3rd Feb 2021 at 15:49, Last updated: 9th Feb 2021 at 10:37

GO Consensus terms

Consensus Hallmark Annotation

Consensus between selected mapping methods.

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Studies: Comparing Cancer Hallmark Descriptions

The number of genes annotated to individual cancer hallmarks

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Created: 8th Feb 2021 at 00:01, Last updated: 9th Feb 2021 at 10:36

Consensus Hallmark Annotation

Additional file 2

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Studies: Comparing Cancer Hallmark Descriptions

Genes annotated to selected GO terms belonging to 4 GO mapping schemes.

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Created: 7th Feb 2021 at 23:58, Last updated: 9th Feb 2021 at 10:36

Consensus Hallmark Annotation

Additional File 1

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Studies: Comparing Cancer Hallmark Descriptions

Download

Created: 7th Feb 2021 at 23:56, Last updated: 9th Feb 2021 at 10:36

Hallmark genes

Consensus Hallmark Annotation

Hallmark gene sets belong to different mapping schemes.

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Studies: Comparing Cancer Hallmark Descriptions

Mapping from pathways to individual cancer hallmarks

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Created: 7th Feb 2021 at 23:45, Last updated: 9th Feb 2021 at 10:35

Consensus Hallmark Annotation

derived from Ulhen's research published in 2017.

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Studies: Comparing Cancer Hallmark Descriptions

Mapping from Gene Ontology terms to individual cancer hallmarks

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Created: 7th Feb 2021 at 20:57, Last updated: 9th Feb 2021 at 10:35

Consensus Hallmark Annotation

The excel presents the mapping from GO terms to individual cancer hallmarks retrieved from selected papers.

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Studies: Comparing Cancer Hallmark Descriptions

The number of annotations belongs to selected GO terms at different time points

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Created: 7th Feb 2021 at 20:52, Last updated: 9th Feb 2021 at 10:34

Consensus Hallmark Annotation

It includes annotation number data at June 2012, June 2016 and Jan 2021.

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

GO hierarchical network comparison between methods

Assays: Analysing Changes to GO Biological Process

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Created: 7th Feb 2021 at 22:31, Last updated: 9th Feb 2021 at 10:34

Consensus Hallmark Annotation

related to Figure 6 and additional file 6

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Mapping from MSigDB pathways to GO terms

Assays: Analysing Changes to GO Biological Process

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Created: 7th Feb 2021 at 20:45, Last updated: 9th Feb 2021 at 10:34

Consensus Hallmark Annotation

No description specified

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Studies: Comparing Cancer Hallmark Descriptions

Edge data of GO terms in 2012

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Created: 8th Feb 2021 at 00:03, Last updated: 9th Feb 2021 at 10:34

Consensus Hallmark Annotation

it can be used to construct the GO network

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

Edge data of GO terms in 2016

Assays: Analysing Changes to GO Biological Process

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Created: 3rd Feb 2021 at 17:00

Consensus Hallmark Annotation

It can be used to construct the GO network

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

species data of GO in 2016

Assays: Analysing Changes to GO Biological Process

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Created: 3rd Feb 2021 at 16:58

Consensus Hallmark Annotation

columns are ' id' , 'ncbi_taxa_id' , 'common_names' , 'lineage_string' , 'genus' , 'species' , 'parent_id' , 'left_value' , 'right_value' , 'taxonomic_rank'.

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus

species data of GO in 2016

Assays: Analysing Changes to GO Biological Process

Download

Created: 3rd Feb 2021 at 16:56

Consensus Hallmark Annotation

columns are ' id' , 'ncbi_taxa_id' , 'common_names' , 'lineage_string' , 'genus' , 'species' , 'parent_id' , 'left_value' , 'right_value' , 'taxonomic_rank'.

Creator: Yi Chen

Submitter: Yi Chen

Investigations: Cancer Hallmark Consensus