CASC3, PGAP1, SLC6A16, CNTNAP4, NPHP1 - These genes are not specific to a single cell type and are expressed in various tissues.
SYCP1, TEX12, REC8, SPO11, SYCP3 - Meiotic Cells
NR5A1, SOX9, FSHR, GATA4 - Sertoli Cells
OTX2, SOX1, TUBB3, PAX6 - Neural Progenitor Cells
Please note that these are general associations and the presence of these genes does not definitively determine the cell type. The exact cell type can depend on the expression levels of these genes and the presence of other marker genes.
Based on the marker genes provided for each row and without conducting a detailed gene expression analysis or referencing a specific database, here's an informed guess for the cell types based on common knowledge in cell biology and gene function:
CASC3, PGAP1, SLC6A16, CNTNAP4, NPHP1 - Given these genes, this profile does not clearly point to a specific, well-known cell type without further context. CNTNAP4 is involved in neuronal activity, but the combination of genes does not provide a clear match. unknown
IL9, SLC30A4, SX18P8, CHRDL2, SMUG1P1 - IL9 is a cytokine involved in immune responses, suggesting these cells might be related to the immune system. However, without a clear connection between all the markers, pinpointing a specific immune cell type is challenging. unknown
HCST, EXOSC8, ORC3, CIDECP2, DNM2 - HCST is involved in the activation of natural killer (NK) cells, suggesting this could be a profile related to NK cells or another cell type involved in the immune response. Natural Killer Cell
DTL, U3, DDX28, WDFY3, PPP1R2P4 - This combination of genes does not correspond to a specific cell type that can be easily identified without further information. These genes are involved in various cellular processes, including DNA repair and synthesis, making it hard to narrow down. unknown
LTK, STK32C, SMIM9, DPPA3P10, MTCO1P12 - LTK is a receptor tyrosine kinase that has been implicated in neuronal development and other processes, but the combination of genes provided does not specify a particular cell type without additional context. unknown
These guesses are made with caution, as identifying cell types solely based on a small set of marker genes without additional context (such as expression levels, cell function, or tissue of origin) can be quite speculative and may not accurately represent the cell types.
Prompt 3 without unknown sentence:
Identifying cell types based on marker gene expression is a nuanced task that requires a deep understanding of gene expression patterns across different tissues and developmental stages. However, I'll provide a general identification of cell types based on the marker genes listed, keeping in mind that the expression of these genes can vary under different conditions and might not be exclusive to a single cell type. Here are potential cell types based on the listed marker genes:
CASC3, PGAP1, SLC6A16, CNTNAP4, NPHP1 - These genes are involved in various cellular functions, including cell adhesion, signaling, and metabolism. Neurons or neural progenitor cells might express these, particularly due to CNTNAP4's involvement in the nervous system.
IL9, SLC30A4, SX18P8, CHRDL2, SMUG1P1 - IL9 is a cytokine that plays roles in various aspects of the immune response. This set of genes could be indicative of T helper cells, specifically Th9 cells, given IL9's role in these cells.
HCST, EXOSC8, ORC3, CIDECP2, DNM2 - HCST is involved in the immune system's activation and signaling pathways. This gene set might suggest Natural Killer (NK) cells due to HCST's significance in NK cell-mediated cytotoxicity.
DTL, U3, DDX28, WDFY3, PPP1R2P4 - These genes are involved in DNA replication, repair, and cell cycle regulation. They could be indicative of cells with high proliferative capacity, such as stem cells or progenitor cells in rapidly renewing tissues.
LTK, STK32C, SMIM9, DPPA3P10, MTCO1P12 - LTK is a receptor tyrosine kinase involved in various cell signaling pathways. This set of genes could suggest endothelial cells due to their roles in vascular development and maintenance.
It's important to note that this identification is very general and should be validated with more specific functional assays or gene expression analyses in the context of the tissue of interest.
Apparently Claude 3 *can* recognize primordial germ cells, bravo! And it wasn't thrown off by the random genes. Theca cells and Leydig cells are very similar, so #8 can get partial credit.
However, for the kinda correct options, the reasoning does include the correct answers:
Row 10: SYCP1, TEX12, REC8, SPO11, SYCP3
SYCP1, SYCP3, REC8, SPO11, TEX12 - Synaptonemal complex components and meiotic recombination proteins. These are highly specific for cells undergoing meiosis. This indicates Meiocyte. (General term for cells undergoing meiosis - can be oocyte or spermatocyte). Considering context of other germ cell types, and general meiotic markers - Spermatocyte or Oocyte is possible, but "Meiocyte" or Germ Cell (Meiotic) is safer more general if just one. Let's go with Spermatocyte for male germline context, or Oocyte precursor for female germline. Given other germ cells identified, Spermatocyte seems more specific.
this was my responses from GTP-4 (I indeed got primordial germ cells for #1)
These are marker genes for different types of human cells. Here are the cell types that these marker genes are associated with:
SOX17, POU5F1, NANOS3, PRDM1, NANOG, CD38 - Primordial Germ Cells
POU5F1, SOX2, KLF4, ITGA6, NANOG - Induced Pluripotent Stem Cells
SOX17, FOXA2, CXCR4, GATA4 - Definitive Endoderm Cells
FOXL2, AMHR2, CD82, NR5A1, FSHR, GATA4 - Granulosa Cells
ZP3, DPPA3, DDX4, NPM2, ZP2 - Oocytes
FOXL2, FSHB, NR5A1, PITX1, GNRHR - Pituitary Gonadotrope Cells
STK31, ZBTB16, DDX4, SSEA4, NANOS2 - Spermatogonial Stem Cells
NR2F2, CYP17A1, STAR, LHCGR, GLI1, HSD3B - Leydig Cells
CASC3, PGAP1, SLC6A16, CNTNAP4, NPHP1 - These genes are not specific to a single cell type and are expressed in various tissues.
SYCP1, TEX12, REC8, SPO11, SYCP3 - Meiotic Cells
NR5A1, SOX9, FSHR, GATA4 - Sertoli Cells
OTX2, SOX1, TUBB3, PAX6 - Neural Progenitor Cells
Please note that these are general associations and the presence of these genes does not definitively determine the cell type. The exact cell type can depend on the expression levels of these genes and the presence of other marker genes.
It's interesting that it didn't say "unknown" for #9, but used a different phrase to represent uncertainty.
Here are GPT-4's responses:
Prompt 1:
Pluripotent Stem Cells
Embryonic Stem Cells
Endoderm Cells
Granulosa Cells
Oocytes
Gonadotroph Cells
Spermatogonial Stem Cells
Leydig Cells
Neuronal Cells
Meiotic Cells
Sertoli Cells
Neural Progenitor Cells
Prompt 2:
Pluripotent Stem Cells
Embryonic Stem Cells
Endoderm Cells
Granulosa Cells
Oocytes
Pituitary Gonadotrope Cells
Germ Cells
Leydig Cells
unknown
Meiotic Cells
Sertoli Cells
Neural Progenitor Cells
Prompt 3:
Based on the marker genes provided for each row and without conducting a detailed gene expression analysis or referencing a specific database, here's an informed guess for the cell types based on common knowledge in cell biology and gene function:
CASC3, PGAP1, SLC6A16, CNTNAP4, NPHP1 - Given these genes, this profile does not clearly point to a specific, well-known cell type without further context. CNTNAP4 is involved in neuronal activity, but the combination of genes does not provide a clear match. unknown
IL9, SLC30A4, SX18P8, CHRDL2, SMUG1P1 - IL9 is a cytokine involved in immune responses, suggesting these cells might be related to the immune system. However, without a clear connection between all the markers, pinpointing a specific immune cell type is challenging. unknown
HCST, EXOSC8, ORC3, CIDECP2, DNM2 - HCST is involved in the activation of natural killer (NK) cells, suggesting this could be a profile related to NK cells or another cell type involved in the immune response. Natural Killer Cell
DTL, U3, DDX28, WDFY3, PPP1R2P4 - This combination of genes does not correspond to a specific cell type that can be easily identified without further information. These genes are involved in various cellular processes, including DNA repair and synthesis, making it hard to narrow down. unknown
LTK, STK32C, SMIM9, DPPA3P10, MTCO1P12 - LTK is a receptor tyrosine kinase that has been implicated in neuronal development and other processes, but the combination of genes provided does not specify a particular cell type without additional context. unknown
These guesses are made with caution, as identifying cell types solely based on a small set of marker genes without additional context (such as expression levels, cell function, or tissue of origin) can be quite speculative and may not accurately represent the cell types.
Prompt 3 without unknown sentence:
Identifying cell types based on marker gene expression is a nuanced task that requires a deep understanding of gene expression patterns across different tissues and developmental stages. However, I'll provide a general identification of cell types based on the marker genes listed, keeping in mind that the expression of these genes can vary under different conditions and might not be exclusive to a single cell type. Here are potential cell types based on the listed marker genes:
CASC3, PGAP1, SLC6A16, CNTNAP4, NPHP1 - These genes are involved in various cellular functions, including cell adhesion, signaling, and metabolism. Neurons or neural progenitor cells might express these, particularly due to CNTNAP4's involvement in the nervous system.
IL9, SLC30A4, SX18P8, CHRDL2, SMUG1P1 - IL9 is a cytokine that plays roles in various aspects of the immune response. This set of genes could be indicative of T helper cells, specifically Th9 cells, given IL9's role in these cells.
HCST, EXOSC8, ORC3, CIDECP2, DNM2 - HCST is involved in the immune system's activation and signaling pathways. This gene set might suggest Natural Killer (NK) cells due to HCST's significance in NK cell-mediated cytotoxicity.
DTL, U3, DDX28, WDFY3, PPP1R2P4 - These genes are involved in DNA replication, repair, and cell cycle regulation. They could be indicative of cells with high proliferative capacity, such as stem cells or progenitor cells in rapidly renewing tissues.
LTK, STK32C, SMIM9, DPPA3P10, MTCO1P12 - LTK is a receptor tyrosine kinase involved in various cell signaling pathways. This set of genes could suggest endothelial cells due to their roles in vascular development and maintenance.
It's important to note that this identification is very general and should be validated with more specific functional assays or gene expression analyses in the context of the tissue of interest.
Thanks! These look better, although GPT-4 still can't recognize primordial germ cells.
Claude 3 Opus:
1. Primordial germ cell
2. Pluripotent stem cell
3. Endoderm cell
4. Granulosa cell
5. Oocyte
6. Gonadotroph
7. Spermatogonial stem cell
8. Leydig cell
9. Unknown
10. Spermatocyte
11. Sertoli cell
12. Neural progenitor cell
Apparently Claude 3 *can* recognize primordial germ cells, bravo! And it wasn't thrown off by the random genes. Theca cells and Leydig cells are very similar, so #8 can get partial credit.
11.5/12 by my count.
I've tested it with Gemini Flash Thinking 2.0 and it responded:
Primordial Germ Cell (correct)
Embryonic Stem Cell (correct)
Definitive Endoderm Cell (correct)
Granulosa Cell (correct)
Oocyte (correct)
Gonadotroph Cell (correct)
Spermatogonial Stem Cell (correct)
Leydig Cell (incorrect, Theca cell)
unknown (correct)
Spermatocyte (sort of correct as said before, markers of mitosis)
Sertoli Cell (correct)
Neuron Precursor Cell (basically correct, but not quite the right term)
However, for the kinda correct options, the reasoning does include the correct answers:
Row 10: SYCP1, TEX12, REC8, SPO11, SYCP3
SYCP1, SYCP3, REC8, SPO11, TEX12 - Synaptonemal complex components and meiotic recombination proteins. These are highly specific for cells undergoing meiosis. This indicates Meiocyte. (General term for cells undergoing meiosis - can be oocyte or spermatocyte). Considering context of other germ cell types, and general meiotic markers - Spermatocyte or Oocyte is possible, but "Meiocyte" or Germ Cell (Meiotic) is safer more general if just one. Let's go with Spermatocyte for male germline context, or Oocyte precursor for female germline. Given other germ cells identified, Spermatocyte seems more specific.
-
Row 12: OTX2, SOX1, TUBB3, PAX6
OTX2, PAX6 - Early neural markers, anterior neural plate, eye field.
SOX1 - Neural precursor marker, early neuroectoderm.
TUBB3 (β-III Tubulin) - Neuron-specific tubulin, marker of neurons and neuronal differentiation. This combination points to Neuron Precursor Cell or Neuroectoderm Cell. Let's choose Neuron Precursor Cell.
-
This is what it got for the incorrect one:
Row 8: NR2F2, CYP17A1, STAR, LHCGR, GLI1, HSD3B
NR2F2 - Adrenal gland development, steroidogenesis.
CYP17A1, STAR, HSD3B - Steroidogenesis enzymes, especially for androgens, progestins, and estrogens.
LHCGR - Luteinizing Hormone/Choriogonadotropin Receptor, on Leydig cells and theca cells.
GLI1 - Hedgehog signaling, can be involved in steroidogenesis regulation.
This combination strongly suggests Leydig Cell.
https://copilot.microsoft.com/ Seems to work even better (using prompt 2)
Here are the cell types corresponding to each row of marker genes:
Primordial Germ Cells
Induced Pluripotent Stem Cells
Definitive Endoderm Cells
Granulosa Cells
Oocytes
Pituitary Gonadotrope Cells
Spermatogonial Stem Cells
Theca Cells
Unknown
Meiotic Cells
Sertoli Cells
Neural Progenitor Cells