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The mitotic progression module only showed marginal prognostic capability within these subtypes.
For example, an alcohol intervention may lead to improved ART adherence, which lowers viral load and extends life expectancy in the progression module.
As expected, knockdown of the mitotic progression module genes resulted in significantly lowered Ki-67 staining as compared to a group of unspecific control siRNAs, suggesting that the mitotic progression genes are pivotal for progression through the cell cycle.
Correspondingly, the mitotic checkpoint module was predictive for distant metastasis free survival (DMFS) within both grade 1 and grade 2 tumors (P = 0.007 and P = 1*10-4, respectively, log-rank tests), whereas the mitotic progression module only was predictestsfor grade 2 tumors (P = 0.001, log-rank test).
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To identify such tumors we investigated correlation between the mitotic checkpoint and progression modules within subgroups of breast cancer [ 23].
By combining Ki-67 intensity data for genes in the mitotic checkpoint and progression modules separately, we could investigate module level effects on proliferation.
To this aim, we calculated the network average clustering co-efficient (NACC) between the mitotic checkpoint and progression modules in luminal samples with known TP53 status [ 48].
Indeed, we observed that while the mitotic checkpoint and progression modules were separated in TP53-wildtype samples they were connected in TP53-mutated samples (P < 0.05).
In addition, low levels of TP53 gene expression correlated to increased interconnectivity between the two mitotic modules in luminal samples, and TP53-mutated luminal samples showed elevated activity of the mitotic checkpoint and progression modules (P = 5*10-4 and P = 9*10-4, t-tests).
Since several of the identified gene expression modules represented processes of broader influence on tumor progression, we assayed module co-expression in seven different cancer forms, including four carcinomas (colon, non-small cell lung carcinoma (NSCLC), ovarian and bladder), stage IV malignant melanoma, diffuse large B-cell lymphoma (DLBCL) and acute myeloid leukemia (AML) (Additional file 2).
Thus, we find close agreement between the experimental results and the model of grooming behavior, both in the progression of cleaning modules down the hierarchical levels and in the ability of modules higher in the hierarchy to suppress the modules below.
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