Title: Bioinformatics Analysis Of Hedgehog Interacting Protein In Colorectal Cancer#A Study
Based On GEO Data And TCGA Data
Version: 0 Date: 06 Jun 2023
Reviewer's report:
In this study, the author analyzed the molecular characteristics of HHIP in colorectal cancer
patients and found that HHIP is low expressed in tumor tissue, and recognizes HHIP related
miRNAs and lncRNAs, which are closely related to immune cells and checkpoints, and may
have a potential role in the immunotherapy of colorectal cancer. This study has clear logic and
reasonable methods, but the results still require extensive editing.
1. In the abstract section, the author describes that "There is growing evidence that Hedgehog
Interaction Protein (HHIP) plays critical roles in the development of severe types of CRC.
However, the specific role and mechanism of HHIP in CRC remains not fully understood. If
HHIP has been found to play a crucial role in various colorectal cancers, there is no need to
explore it.
2. In the method section, what is the threshold for differential expression analysis used by
GEO2R, which should be described by the author.
3. In order to enrich the research results, it is recommended that the author search for
immunohistochemical results of HHIP between colorectal cancer and normal tissues in the HPA
database to confirm its differential expression at the protein level.
4. In order to explore the biological processes involved in the HHIP gene, the author can use
GSEA to conduct gene enrichment analysis of a single gene to confirm the impact of HHIP on
the occurrence and development of colorectal cancer.
5. The HHIP gene has been found to be associated with the prognosis of colorectal cancer
patients. It is recommended that the author add a correlation analysis between clinical features
and the expression level of this gene, including molecular typing and tumor staging of colorectal
cancer.
6. For the characterization of HHIP gene, the author can also use the DNA methylation data in
the TCGA database to analyze the change of DNA methylation level in the promoter region of
HHIP gene and whether it affects the gene expression level.
7. For the correlation analysis between HHIP and immunity, it is suggested that the author
can add correlation analysis between HHIP and immune pathway activity, use ssGSEA method
to calculate immune pathway activity, and analyze the correlation between immune pathway
activity and HHIP.
8. Figure 3 only has one lncRNA expression differential analysis and cannot be displayed as a
main graph. It is recommended that the author combine this graph with Figure 2.
9. Both Table 2 and Table 3 suggest that the author use a three line table for presentation.
Title: Bioinformatics Analysis Of Hedgehog Interacting Protein In Colorectal Cancer#A Study
Based On GEO Data And TCGA Data
Version: 0 Date: 06 Jun 2023
Reviewer's report:
In this study, the author analyzed the molecular characteristics of HHIP in colorectal cancer
patients and found that HHIP is low expressed in tumor tissue, and recognizes HHIP related
miRNAs and lncRNAs, which are closely related to immune cells and checkpoints, and may
have a potential role in the immunotherapy of colorectal cancer. This study has clear logic and
reasonable methods, but the results still require extensive editing.
1. In the abstract section, the author describes that "There is growing evidence that Hedgehog
Interaction Protein (HHIP) plays critical roles in the development of severe types of CRC.
However, the specific role and mechanism of HHIP in CRC remains not fully understood. If
HHIP has been found to play a crucial role in various colorectal cancers, there is no need to
explore it.
2. In the method section, what is the threshold for differential expression analysis used by
GEO2R, which should be described by the author.
3. In order to enrich the research results, it is recommended that the author search for
immunohistochemical results of HHIP between colorectal cancer and normal tissues in the HPA
database to confirm its differential expression at the protein level.
4. In order to explore the biological processes involved in the HHIP gene, the author can use
GSEA to conduct gene enrichment analysis of a single gene to confirm the impact of HHIP on
the occurrence and development of colorectal cancer.
5. The HHIP gene has been found to be associated with the prognosis of colorectal cancer
patients. It is recommended that the author add a correlation analysis between clinical features
and the expression level of this gene, including molecular typing and tumor staging of colorectal
cancer.
6. For the characterization of HHIP gene, the author can also use the DNA methylation data in
the TCGA database to analyze the change of DNA methylation level in the promoter region of
HHIP gene and whether it affects the gene expression level.
7. For the correlation analysis between HHIP and immunity, it is suggested that the author
can add correlation analysis between HHIP and immune pathway activity, use ssGSEA method
to calculate immune pathway activity, and analyze the correlation between immune pathway
activity and HHIP.
8. Figure 3 only has one lncRNA expression differential analysis and cannot be displayed as a
main graph. It is recommended that the author combine this graph with Figure 2.
9. Both Table 2 and Table 3 suggest that the author use a three line table for presentation.
Please review this paper.
user
Title: Bioinformatics Analysis Of Hedgehog Interacting Protein In Colorectal Cancer#A Study
Based On GEO Data And TCGA Data
Version: 0 Date: 06 Jun 2023
Reviewer's report:
In this study, the author analyzed the molecular characteristics of HHIP in colorectal cancer
patients and found that HHIP is low expressed in tumor tissue, and recognizes HHIP related
miRNAs and lncRNAs, which are closely related to immune cells and checkpoints, and may
have a potential role in the immunotherapy of colorectal cancer. This study has clear logic and
reasonable methods, but the results still require extensive editing.
1. In the abstract section, the author describes that "There is growing evidence that Hedgehog
Interaction Protein (HHIP) plays critical roles in the development of severe types of CRC.
However, the specific role and mechanism of HHIP in CRC remains not fully understood. If
HHIP has been found to play a crucial role in various colorectal cancers, there is no need to
explore it.
2. In the method section, what is the threshold for differential expression analysis used by
GEO2R, which should be described by the author.
3. In order to enrich the research results, it is recommended that the author search for
immunohistochemical results of HHIP between colorectal cancer and normal tissues in the HPA
database to confirm its differential expression at the protein level.
4. In order to explore the biological processes involved in the HHIP gene, the author can use
GSEA to conduct gene enrichment analysis of a single gene to confirm the impact of HHIP on
the occurrence and development of colorectal cancer.
5. The HHIP gene has been found to be associated with the prognosis of colorectal cancer
patients. It is recommended that the author add a correlation analysis between clinical features
and the expression level of this gene, including molecular typing and tumor staging of colorectal
cancer.
6. For the characterization of HHIP gene, the author can also use the DNA methylation data in
the TCGA database to analyze the change of DNA methylation level in the promoter region of
HHIP gene and whether it affects the gene expression level.
7. For the correlation analysis between HHIP and immunity, it is suggested that the author
can add correlation analysis between HHIP and immune pathway activity, use ssGSEA method
to calculate immune pathway activity, and analyze the correlation between immune pathway
activity and HHIP.
8. Figure 3 only has one lncRNA expression differential analysis and cannot be displayed as a
main graph. It is recommended that the author combine this graph with Figure 2.
9. Both Table 2 and Table 3 suggest that the author use a three line table for presentation.
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