update README_cn

README_cn.md

@@ -61,45 +61,40 @@ res
 
 例如:
 ```markdown
-# Most Possible celltypes
-### Geneset 0: CD4+ T Helper Cells
-**gene marker**: CD3D, CD3E, CCR7, CD27
-**reason**: The presence of CD3D and CD3E, which are integral components of the T-cell receptor complex, along with CCR7 and CD27, which are characteristic of naïve and central memory CD4+ T helper cells, strongly supports this cell type.
-**cell state/subtype**: Memory or naïve CD4+ T helper cells in a resting or surveillance state, ready to respond to antigenic challenges.
-
-### Geneset 1: B Cells
-**gene marker**: CD79A, MS4A1, CD79B, CD74, CD37
-**reason**: These markers are highly specific to B lymphocytes, with CD79A and CD79B being components of the B-cell receptor complex, MS4A1 (CD20) being a well-known B-cell marker, and CD74 and CD37 also being commonly expressed in B cells.
-**cell state/subtype**: Mature B cells, potentially activated and capable of antigen presentation, indicated by the presence of HLA-DRA.
-
-### Geneset 2: Monocytes/Macrophages
-**gene marker**: FCGR3A, FCER1G, AIF1, LILRA3, MT2A
-**reason**: The combination of FCGR3A (CD16), FCER1G (part of Fc receptor complex), AIF1 (involved in macrophage activation), LILRA3 (implicated in immune regulation), and MT2A (a metal detoxification protein) strongly indicates monocytes/macrophages.
-**cell state/subtype**: Activated monocytes/macrophages, possibly responding to inflammation or infection.
-
-### Geneset 3: Natural Killer (NK) cells
-**gene marker**: GNLY, GZMB, NKG7, PRF1, FCGR3A, TYROBP, XCL2, GZMA
-**reason**: This set includes key markers of NK cell function, such as cytotoxic granule proteins (granzymes, perforin), signaling molecules (TYROBP), and the activating receptor CD16 (FCGR3A).
-**cell state/subtype**: Activated NK cells, capable of cytotoxic activity against infected or transformed cells.
-
-### Geneset 4: Cytotoxic T Cells (CD8+)
-**gene marker**: CCL5, GZMK, NKG7, CST7, CD3D, GZMA, CTSW, CD8A, KLRG1, GZMH, NCR3
-**reason**: The presence of CD8A, granzymes (GZMA, GZMK, GZMH), NKG7, and KLRG1 indicates cytotoxic T cells, which are known for their direct killing of infected or cancerous cells.
-**cell state/subtype**: Activated or effector CD8+ T cells, potentially engaged in immune surveillance or responding to recent antigen exposure in a healthy individual.
-### Geneset 5 : Monocytes/Macrophages
-**gene marker**: S100A8, LYZ, S100A9, LGALS2, FCN1, CD14, GSTP1, FTL, TYROBP, GRN, APOBEC3A, GPX1
-**reason**: The presence of a comprehensive set of markers, including S100A8, S100A9, CD14, and LYZ, strongly suggests monocytes/macrophages. These markers are indicative of both the cell lineage and the inflammatory state typical of these cells in response to stimuli.
-**cell state/subtype**: Activated or inflammatory state due to the presence of alarmins and other inflammatory markers, indicating a response to infection or inflammation.
-
-### Geneset 6 : Dendritic Cells
-**gene marker**: HLA-DQA1, HLA-DPB1, HLA-DQB1, HLA-DRA, HLA-DPA1, HLA-DRB1, HLA-DRB5, CD74
-**reason**: The high expression of MHC class II genes (HLA-DQA1, HLA-DPB1, etc.) and CD74, which is crucial for MHC class II antigen presentation, is characteristic of dendritic cells. These markers are essential for the function of antigen presentation to T cells.
-**cell state/subtype**: Activated or mature dendritic cells, as indicated by the upregulation of MHC class II molecules, which occurs during the maturation process triggered by pathogen recognition.
-
-### Geneset 7 : Platelets
-**gene marker**: PPBP, PF4, GP9, GNG11
-**reason**: The expression of PPBP, PF4, and GP9 is highly specific to platelets, which are crucial for hemostasis and thrombosis. GNG11, while not exclusive, supports the presence of platelet-related functions.
-**cell state/subtype**: Activated or resting platelets. Given the presence of markers associated with platelet function and aggregation, these platelets might be in a state ready to respond to vascular damage or inflammation.
+# CellType Analysis
+## cluster geneset 0
+
+### Gene List
+\```
+LDHB, LTB, RGCC, IL32, NOSIP, CD3D, CD3E, TMEM123, VIM, TMEM66, FYB, JUNB, CCR7, CD27, MYL12A
+\```
+
+### Celltype Prediction
+#### Optimal Celltype: T Cells (likely CD4+ T cells)
+**Key Markers**:
+- Cell-specific: CD3D, CD3E, CCR7, CD27, FYB
+- Context-specific: LTB, JUNB, VIM
+
+**Evidence and Reasoning**
+- **PRIMARY EVIDENCE**: The presence of CD3D and CD3E, which are essential components of the T cell receptor complex, strongly indicates a T cell population. These markers are highly specific to T cells.
+- **SECONDARY EVIDENCE**: CCR7 is a chemokine receptor that is typically expressed on naïve and central memory T cells, suggesting that these cells may be in a non-activated or memory state.
+- **ADDITIONAL EVIDENCE**: CD27 and FYB are also known to be expressed in T cells, particularly in activated T cells. LTB (lymphotoxin beta) and JUNB (a transcription factor) are involved in T cell activation and function.
+
+**Validation**: Other gold standard markers for T cells (not in Geneset 0) include CD4, CD8, and TCRα/β. For CD4+ T cells, additional markers like CD45RA and CD45RO can be used to distinguish between naïve and memory T cells.
+
+#### Alternative Considerations
+- **Alternative celltype1: NK cells**
+    - **WHY Alternative? Key MARKERS, Evidence and Reasoning**: NK cells can express some of the markers found in this geneset, such as CCR7 and CD27, but the presence of CD3D and CD3E, which are not expressed in NK cells, makes this less likely.
+    - **OTHER Gold Standard MARKERS(NOT IN Geneset 0) TO VALIDATE THE Alternative celltype1**: NK cells would typically express NKp46, KIRs, and NKG2D, which are not present in this geneset.
+
+- **Alternative celltype2: B cells**
+    - **WHY Alternative? Key MARKERS, Evidence and Reasoning**: B cells do not typically express CD3D and CD3E, which are strong T cell markers. However, some B cell markers like CD27 and CCR7 are present, which might lead to confusion. The absence of B cell-specific markers like CD19 and CD20 makes this alternative less likely.
+    - **OTHER Gold Standard MARKERS(NOT IN Geneset 0) TO VALIDATE THE Alternative celltype2**: B cells would typically express CD19, CD20, and surface IgM, which are not present in this geneset.
+
+### Novel Insights
+- **NOTEWORTHY PATTERNS**: The co-expression of CCR7 and CD27 suggests a population of T cells that are either naïve or central memory T cells.
+- **CELL STATE**: The expression of JUNB and LTB, along with other activation-related genes, suggests that these T cells may be in an activated or recently activated state.
+- **POTENTIAL NEW FINDINGS**: The presence of VIM (vimentin), a marker often associated with mesenchymal cells, in T cells is intriguing and could indicate a unique subset of T cells or a state of T cells that have undergone some form of stress or activation leading to the upregulation of vimentin.
 
 ```