Table · dataset · 2024
Unbiased Phenotype Detection Using Negative Controls data set
Listed in Edmond
Phenotypic screens using automated microscopy allow comprehensive measurement of the effects of compounds on cells due to the number of markers that can be scored and the richness of the parameters that can be extracted.
Description
The high dimensionality of the data is both a rich source of information and a source of noise that might hide information. Many methods have been proposed to deal with this complex data in order to reduce the complexity and identify interesting phenotypes.
Nevertheless, the majority of laboratories still only use one or two parameters in their analysis, likely due to the computational challenges of carrying out a more sophisticated analysis. Here, we present a novel method that allows discovering new, previously unknown phenotypes based on negative controls only. The method is compared with L1-norm regularization, a standard method to obtain a sparse matrix.
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The analytical pipeline is implemented in the open-source software KNIME, allowing the implementation of the method in many laboratories, even ones without advanced computing knowledge. As the data set for this paper is large we recommend using a download tool (or browser) that is capable of resuming. PubMed ID 30616488 WebOfScience Link WOS:000459287100004
Links
Where it is published
- Dataverse dataset page edmond.mpg.de/dataset.xhtml?persistentId=doi%3A10.17617%2F3.US5BBT ↗
landing page · from edmond mpdl mpg de
- DOI doi.org/10.17617/3.us5bbt ↗
DOI / persistent id · from edmond mpdl mpg de
Catalogue records · 1
- Dataverse API edmond.mpg.de/api/datasets/:persistentId/?persistentId=doi%3A10.17617%2F3.US… ↗
metadata API · from edmond mpdl mpg de
Topics
- From keywords
- Astronomy & Astrophysics · Chemistry · Computer Science & AI · Earth & Environmental Science · Economics & Finance · Engineering · Humanities · Life Sciences · Life Sciences · Materials Science · Medicine & Health · Ocean & Atmospheric Science · Physics · Social Science
- Inferred from text
- Microscopy 75% · Oncology and carcinogenesis 70%
Provenance · 2 source records, 24 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Edmond | doi:10.17617/3.US5BBT | 12 d ago | JSON v1 |
| Edmond | doi:10.17617/3.US5BBT | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].anzsrc:group:3211 | enrichment · edmond mpdl mpg de | taxonomy-embedding@1.0.0 | title+keywords+description (70%) |
| concepts[field].dataverse_subject:biology | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | /subjects |
| concepts[field].dataverse_subject:biology | source · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:astronomy | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:chemistry | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:computer-science-ai | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:earth-environmental | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:economics-finance | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:engineering | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:humanities | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:materials-science | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:ocean-atmospheric | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:physics | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:social-science | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[modality].local:modality:microscopy | enrichment · edmond mpdl mpg de | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | |
| description | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | /description |
| publication_date | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | |
| title | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | /name |
| updated_date | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | |
| version_label | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 |