LymphTF-DB: a database of transcription factors involved in lymphocyte development

Childress, Paul; Fletcher, R L; Perumal, Narayanan B.

doi:10.1038/sj.gene.6364386

Cited by 10 publications

(7 citation statements)

References 45 publications

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“…Meanwhile, many genes involved in these branches (i.e., IL1RN encoding IL1, IL1R1, IL1R2 encoding IL1R, MAPK11, MAPK13 encoding p38MAPK, JUN encoding c-JUN, FOS encoding c-FOS, MYC encoding c-MYC, STAT3 encoding STAT3) were also upregulated, indicating that they may promote hepatocyte G0/G1 transition of the cell cycle. These results are supported by Morello et al who have shown that MYC is the immediate early proto-oncogene that could rapidly express after partial hepatectomy and promote cells transition from G0 to G1 phase [14], and the research of Masato et al, who showed that STAT3 and NFIL6 promote HC G0/G1 transition after phosphorylation by ERK and JAK [31]. In addition, target genes such as CTGF, MED1, and SOX15 (Table 4) have also shown positive regulation of G0/G1 transition by Gene Ontology, which is consistent with our results in Fig.…”

Section: Discussionsupporting

confidence: 77%

“…To determine the activity level of each signaling pathway and its branches, we used the Et to analyze the signaling activity as described in the Materials and Methods section. To confirm the interaction relationships between G0/G1 signaling pathways and HC G0/G1 transition, transcription factors of G0/G1 transition signaling pathways constructed above were input into TRED and Lymph TF-DB [30,31] to find their downstream target genes. Then the Et value of G0/G1 transition activity was calculated according to the section "Analysis of gene synergy (Et)" above.…”

Section: Analysis Of Gene Synergy (Et)mentioning

confidence: 99%

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Study on the activity of the signaling pathways regulating hepatocytes from G0 phase into G1 phase during rat liver regeneration

Li¹,

Zhou²,

Mei³

et al. 2014

Cellular and Molecular Biology Letters

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Under normal physiological conditions, the majority of hepatocytes are in the functional state (G0 phase). After injury or liver partial hepatectomy (PH), hepatocytes are rapidly activated to divide. To understand the mechanism underlying hepatocyte G0/G1 transition during rat liver regeneration, we used the Rat Genome 230 2.0 Array to determine the expression changes of genes, then searched the GO and NCBI databases for genes associated with the G0/G1 transition, and QIAGEN and KEGG databases for the G0/G1 transition signaling pathways. We used expression profile function (E t) to calculate the activity level of the known G0/G1 transition signal pathways, and Ingenuity Pathway Analysis 9.0 (IPA) to determine the interactions among these signaling pathways. The results of our study show that the activity of the signaling pathways of HGF, IL-10 mediated by p38MAPK, IL-6 mediated by STAT3, and JAK/STAT mediated by Ras/ERK and STAT3 are significantly increased during the priming phase (2–6 h after PH) of rat liver regeneration. This leads us to conclude that during rat liver regeneration, the HGF, IL-10, IL-6 and JAK/STAT signaling pathways play a major role in promoting hepatocyte G0/G1 transition in the regenerating liver.

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Section: Discussionsupporting

confidence: 77%

Section: Analysis Of Gene Synergy (Et)mentioning

confidence: 99%

Study on the activity of the signaling pathways regulating hepatocytes from G0 phase into G1 phase during rat liver regeneration

Li¹,

Zhou²,

Mei³

et al. 2014

Cellular and Molecular Biology Letters

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“…genmapp.org), KEGG (www.genome.jp/kegg/pathway.html), and QIAGEN (www.qiagen.com/ geneglobe/pathways.aspx) (Salomonis et al, 2007;Antonov et al, 2010). Moreover, NF-κB signaling pathway-related genes, such as Nfkb, Nfkb2,Rela,Relb,, were input into TRED (http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=searchTFGeneForm), lymph TFDB (http:// www.iupui.edu/~tfinterx/activity.php) and into NF-kB (http://www.bu.edu/nf-kb/gene-resources/ target-genes/) to find out their downstream target genes in rat (Childress et al, 2007;Jiang et al, 2007), mouse and human, among which cell proliferation-related genes were identified with the NCBI database. In the end, the genes were reconfirmed through literature searches of pertinent articles.…”

Section: Identification Of Nf-κb Signaling Pathway-and Cell Proliferamentioning

confidence: 99%

Branches of NF-κb signaling pathway regulate hepatocyte proliferation in rat liver regeneration

et al. 2015

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ABSTRACT. Previous studies have demonstrated that the nuclear factor κB (NF-κB) pathway is involved in promoting cell proliferation. To further explore the regulatory branches and their sequence in the NF-κB pathway in the promotion of hepatocyte proliferation at the transcriptional level during rat liver regeneration, Rat Genome 230 2.0 array was used to detect the expression changes of the isolated hepatocytes. We found that many genes involved in the NF-κB pathway (including 73 known genes and 19 homologous genes) and cell proliferation (including 484 genes and 104 homologous genes) were associated with liver regeneration. Expression profile function (E p ) was used to analyze the biological processes. It was revealed that the NF-κB pathway promoted hepatocyte proliferation through three branches. Several methods of integrated statistics were applied to extract and screen key genes in liver regeneration, and it indicated that eight genes may play a vital role in rat liver regeneration. To confirm the above predicted results, Ccnd1, Jun and Myc were analyzed using qRT-PCR, and the results were generally consistent with that of microarray data. It is concluded that 3 branches and 8 key genes involved in the NF-κB pathway regulate hepatocyte proliferation during rat liver regeneration.

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“…The list of genes found during the initial search, was subsequently compared to and complemented with genes in the biological pathway maps found in GENMAPP (www.genmapp.org), KEGG (www.genome.jp/ kegg/pathway.html), and QIAGEN (www.qiagen.com/geneglobe/path ways.aspx) (Salomonis et al, 2007;Antonov et al, 2010). Moreover, NF-kB signaling pathway-related genes, such as NFKB1, NFKB2, RelA, RelB, and c-Rel, were input into TRED (http://rulai.cshl.edu/cgi-bin/TRED/ tred.cgi?process=searchTFGeneForm), LymphTF-DB (http://www.iupui.edu/tfinterx/activity.php), and NF-kB (www.bu.edu) (Childress et al, 2007;Jiang et al, 2007). This was done to find their downstream target genes in rat, mouse, and human, among which cell proliferation-related genes were identified with the NCBI database, and reconfirmed with published articles.…”

Section: Identification Of Nf-κb Signaling Pathway-and Cell Proliferamentioning

confidence: 99%

Branches of the NF-κB signaling pathway regulate proliferation of oval cells in rat liver regeneration

Zhao¹,

Qin²,

Niu³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. The NF-kB (nuclear factor kB) pathway is involved in the proliferation of many cell types. To explore the mechanism of the NF-kB signaling pathway underlying the oval cell proliferation during rat liver regeneration, the Rat Genome 230 2.0 Array was used to detect expression changes of NF-kB signaling pathway-related genes in oval cells. The results revealed that the expression levels of many genes in the NF-kB pathway were significantly changed. This included 48 known genes and 16 homologous genes, as well as 370 genes and 85 homologous genes related to cell proliferation. To further understand the biological significance of these changes, an expression profile function was used to analyze the potential biological processes. The results showed that the NF-kB pathway promoted oval cell proliferation mainly through three signaling branches; the tumor necrosis factor alpha branch (TNF-a pathway), the growth factor branch, and the chemokine branch. An integrated statistics method was used to define the key genes in the NF-kB pathway. Seven genes were identified to play vital roles in the NF-kB pathway. To confirm these results, the protein content, including two key genes (TNF and FGF11) and two nonkey genes (CCL2 and TNFRSF12A), were analyzed using two-dimensional gel electrophoresis and MALDI-TOF/TOF mass spectrometry. The results were generally consistent with those of the array data. To conclude, three branches and seven key genes were involved in the NF-kB signaling pathway that regulates oval cell proliferation during rat liver regeneration.

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LymphTF-DB: a database of transcription factors involved in lymphocyte development

Cited by 10 publications

References 45 publications

Study on the activity of the signaling pathways regulating hepatocytes from G0 phase into G1 phase during rat liver regeneration

Study on the activity of the signaling pathways regulating hepatocytes from G0 phase into G1 phase during rat liver regeneration

Branches of NF-κb signaling pathway regulate hepatocyte proliferation in rat liver regeneration

Branches of the NF-κB signaling pathway regulate proliferation of oval cells in rat liver regeneration

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