Identification of potential transcription factor and protein kinases for regulation of differentially expressed genes for fluoride exposure in human using Expression2Kinases (X2K) approach

Choudhari, Jyoti Kant; Sahariah, Biju Prava; Choubey, Jyotsna; Patel, Anna; Verma, Mukesh

doi:10.1007/s13721-017-0148-7

Cited by 2 publications

(2 citation statements)

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“…Cluster 1 includes proteins CASP3, CASP9, BAX, TP53, BAD, GSK3B, POU5F1, MAPK14, CREB1, SOX2, and KLF4. Gene ontology data show that these proteins are associated with amyotrophic lateral sclerosis (hsa05014) [55], colorectal cancer (hsa05210) [56], and positive regulation of neuron death (GO: 1901216) [57].…”

Section: Resultsmentioning

confidence: 99%

“…Cluster 2 genes are mentioned in Table 3. GO analysis shows that these proteins belong to thyroid hormone signaling pathway (hsa04919) [55], diseases of signal transduction (R-HSA-5663202) [56], and pathways in cancer (hsa05200) [57]. Cluster 3 proteins are involved in pathways of toxoplasmosis (hsa05145) [55], tuberculosis (hsa05152) [56], and fluid shear stress and atherosclerosis (hsa05418) [55].…”

Section: Resultsmentioning

confidence: 99%

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Clustering, Pathway Enrichment, and Protein-Protein Interaction Analysis of Gene Expression in Neurodevelopmental Disorders

Yadav

Srivastava

2018

Advances in Pharmacological Sciences

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Neuronal developmental disorder is a class of diseases in which there is impairment of the central nervous system and brain function. The brain in its developmental phase undergoes tremendous changes depending upon the stage and environmental factors. Neurodevelopmental disorders include abnormalities associated with cognitive, speech, reading, writing, linguistic, communication, and growth disorders with lifetime effects. Computational methods provide great potential for betterment of research and insight into the molecular mechanism of diseases. In this study, we have used four samples of microarray neuronal developmental data: control, RV (resveratrol), NGF (nerve growth factor), and RV + NGF. By using computational methods, we have identified genes that are expressed in the early stage of neuronal development and also involved in neuronal diseases. We have used MeV application to cluster the raw data using distance metric Pearson correlation coefficient. Finally, 60 genes were selected on the basis of coexpression analysis. Further pathway analysis was done using the Metascape tool, and the biological process was studied using gene ontology database. A total of 13 genes AKT1, BAD, BAX, BCL2, BDNF, CASP3, CASP8, CASP9, MYC, PIK3CD, MAPK1, MAPK10, and CYCS were identified that are common in all clusters. These genes are involved in neuronal developmental disorders and cancers like colorectal cancer, apoptosis, tuberculosis, amyotrophic lateral sclerosis (ALS), neuron death, and prostate cancer pathway. A protein-protein interaction study was done to identify proteins that belong to the same pathway. These genes can be used to design potential inhibitors against neurological disorders at the early stage of neuronal development. The microarray samples discussed in this publication are part of the data deposited in NCBI's Gene Expression Omnibus (Yadav et al., 2018) and are accessible through GEO Series (accession number GSE121261).

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Section: Resultsmentioning

confidence: 99%