SEMA3D Gene

HGNC Family	Immunoglobulin superfamily domain containing, Semaphorins (SEMA)
Name	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D
Description	This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nA careful review of the 44 abstracts provided—spanning investigations into mitochondrial biogenesis, energy metabolism, substrate utilization, and the transcriptional control mediated by PGC‑1α in tissues such as skeletal muscle, liver, heart, and brain ["}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "44"}]}, {"type": "t", "text": "—none make any mention of SEMA3D. \n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn other words, while these studies richly detail the pivotal roles of PGC‑1α and its network of signaling partners in modulating oxidative metabolism, mitochondrial function, and tissue-specific adaptive responses to diverse physiological stresses, they do not provide any data or commentary regarding SEMA3D. SEMA3D—a member of the semaphorin family typically associated with axon guidance and neuronal patterning—is not discussed in any fragment of the literature presented here. As such, no summary of SEMA3D’s function (or its potential contributions to cellular signaling, development, or disease) can be derived from this collection, and clarification or additional sources would be required to appraise its biological role.\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "S Herzig, F Long, U S Jhala, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CREB regulates hepatic gluconeogenesis through the coactivator PGC-1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2001)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/35093131"}], "href": "https://doi.org/10.1038/35093131"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "11557984"}], "href": "https://pubmed.ncbi.nlm.nih.gov/11557984"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Jiandie Lin, Hai Wu, Paul T Tarr, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Transcriptional co-activator PGC-1 alpha drives the formation of slow-twitch muscle fibres."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2002)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature00904"}], "href": "https://doi.org/10.1038/nature00904"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12181572"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12181572"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "James Rhee, Yusuke Inoue, J Cliff Yoon, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Regulation of hepatic fasting response by PPARgamma coactivator-1alpha (PGC-1): requirement for hepatocyte nuclear factor 4alpha in gluconeogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.0730870100"}], "href": "https://doi.org/10.1073/pnas.0730870100"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12651943"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12651943"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Pere Puigserver, James Rhee, Jerry Donovan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Insulin-regulated hepatic gluconeogenesis through FOXO1-PGC-1alpha interaction."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature01667"}], "href": "https://doi.org/10.1038/nature01667"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12754525"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12754525"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Christoph Handschin, James Rhee, Jiandie Lin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "An autoregulatory loop controls peroxisome proliferator-activated receptor gamma coactivator 1alpha expression in muscle."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.1232352100"}], "href": "https://doi.org/10.1073/pnas.1232352100"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12764228"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12764228"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Vamsi K Mootha, Christoph Handschin, Dan Arlow, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.0401401101"}], "href": "https://doi.org/10.1073/pnas.0401401101"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15100410"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15100410"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Seung-Hoi Koo, Hiroaki Satoh, Stephan Herzig, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PGC-1 promotes insulin resistance in liver through PPAR-alpha-dependent induction of TRB-3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Med (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nm1044"}], "href": "https://doi.org/10.1038/nm1044"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15107844"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15107844"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Jiandie Lin, Pei-Hsuan Wu, Paul T Tarr, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Defects in adaptive energy metabolism with CNS-linked hyperactivity in PGC-1alpha null mice."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2004.09.013"}], "href": "https://doi.org/10.1016/j.cell.2004.09.013"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15454086"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15454086"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Janice M Huss, Inés Pineda Torra, Bart Staels, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Estrogen-related receptor alpha directs peroxisome proliferator-activated receptor alpha signaling in the transcriptional control of energy metabolism in cardiac and skeletal muscle."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.24.20.9079-9091.2004"}], "href": "https://doi.org/10.1128/MCB.24.20.9079-9091.2004"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15456881"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15456881"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Joseph T Rodgers, Carlos Lerin, Wilhelm Haas, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Nutrient control of glucose homeostasis through a complex of PGC-1alpha and SIRT1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature03354"}], "href": "https://doi.org/10.1038/nature03354"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15744310"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15744310"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Teresa C Leone, John J Lehman, Brian N Finck, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PGC-1alpha deficiency causes multi-system energy metabolic derangements: muscle dysfunction, abnormal weight control and hepatic steatosis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS Biol (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pbio.0030101"}], "href": "https://doi.org/10.1371/journal.pbio.0030101"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15760270"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15760270"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "Takayuki Akimoto, Steven C Pohnert, Ping Li, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Exercise stimulates Pgc-1alpha transcription in skeletal muscle through activation of the p38 MAPK pathway."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M408862200"}], "href": "https://doi.org/10.1074/jbc.M408862200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15767263"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15767263"}]}, {"type": "r", "ref": 13, "children": [{"type": "t", "text": "Zoltan Arany, Huamei He, Jiandie Lin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Transcriptional coactivator PGC-1 alpha controls the energy state and contractile function of cardiac muscle."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Metab (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cmet.2005.03.002"}], "href": "https://doi.org/10.1016/j.cmet.2005.03.002"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16054070"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16054070"}]}, {"type": "r", "ref": 14, "children": [{"type": "t", "text": "Adam R Wende, Janice M Huss, Paul J Schaeffer, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PGC-1alpha coactivates PDK4 gene expression via the orphan nuclear receptor ERRalpha: a mechanism for transcriptional control of muscle glucose metabolism."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.25.24.10684-10694.2005"}], "href": "https://doi.org/10.1128/MCB.25.24.10684-10694.2005"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16314495"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16314495"}]}, {"type": "r", "ref": 15, "children": [{"type": "t", "text": "Woo Je Lee, Mina Kim, Hye-Sun Park, et al. "}, {"type": "b", "children": [{"type": "t", "text": "AMPK activation increases fatty acid oxidation in skeletal muscle by activating PPARalpha and PGC-1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochem Biophys Res Commun (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bbrc.2005.12.011"}], "href": "https://doi.org/10.1016/j.bbrc.2005.12.011"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16364253"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16364253"}]}, {"type": "r", "ref": 16, "children": [{"type": "t", "text": "Marc Uldry, Wenli Yang, Julie St-Pierre, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Complementary action of the PGC-1 coactivators in mitochondrial biogenesis and brown fat differentiation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Metab (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cmet.2006.04.002"}], "href": "https://doi.org/10.1016/j.cmet.2006.04.002"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16679291"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16679291"}]}, {"type": "r", "ref": 17, "children": [{"type": "t", "text": "Carles Lerin, Joseph T Rodgers, Dario E Kalume, et al. "}, {"type": "b", "children": [{"type": "t", "text": "GCN5 acetyltransferase complex controls glucose metabolism through transcriptional repression of PGC-1alpha."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Metab (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cmet.2006.04.013"}], "href": "https://doi.org/10.1016/j.cmet.2006.04.013"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16753578"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16753578"}]}, {"type": "r", "ref": 18, "children": [{"type": "t", "text": "Zoltan Arany, Mikhail Novikov, Sherry Chin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Transverse aortic constriction leads to accelerated heart failure in mice lacking PPAR-gamma coactivator 1alpha."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.0603615103"}], "href": "https://doi.org/10.1073/pnas.0603615103"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16775082"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16775082"}]}, {"type": "r", "ref": 19, "children": [{"type": "t", "text": "Libin Cui, Hyunkyung Jeong, Fran Borovecki, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Transcriptional repression of PGC-1alpha by mutant huntingtin leads to mitochondrial dysfunction and neurodegeneration."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2006.09.015"}], "href": "https://doi.org/10.1016/j.cell.2006.09.015"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17018277"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17018277"}]}, {"type": "r", "ref": 20, "children": [{"type": "t", "text": "Marco Sandri, Jiandie Lin, Christoph Handschin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PGC-1alpha protects skeletal muscle from atrophy by suppressing FoxO3 action and atrophy-specific gene transcription."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.0607795103"}], "href": "https://doi.org/10.1073/pnas.0607795103"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17053067"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17053067"}]}, {"type": "r", "ref": 21, "children": [{"type": "t", "text": "Julie St-Pierre, Stavit Drori, Marc Uldry, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Suppression of reactive oxygen species and neurodegeneration by the PGC-1 transcriptional coactivators."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2006.09.024"}], "href": "https://doi.org/10.1016/j.cell.2006.09.024"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17055439"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17055439"}]}, {"type": "r", "ref": 22, "children": [{"type": "t", "text": "Christoph Handschin, Yvonne M Kobayashi, Sherry Chin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PGC-1alpha regulates the neuromuscular junction program and ameliorates Duchenne muscular dystrophy."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Dev (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gad.1525107"}], "href": "https://doi.org/10.1101/gad.1525107"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17403779"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17403779"}]}, {"type": "r", "ref": 23, "children": [{"type": "t", "text": "Chang Liu, Siming Li, Tiecheng Liu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Transcriptional coactivator PGC-1alpha integrates the mammalian clock and energy metabolism."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature05767"}], "href": "https://doi.org/10.1038/nature05767"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17476214"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17476214"}]}, {"type": "r", "ref": 24, "children": [{"type": "t", "text": "Xinghai Li, Bobby Monks, Qingyuan Ge, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Akt/PKB regulates hepatic metabolism by directly inhibiting PGC-1alpha transcription coactivator."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature05861"}], "href": "https://doi.org/10.1038/nature05861"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17554339"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17554339"}]}, {"type": "r", "ref": 25, "children": [{"type": "t", "text": "Christoph Handschin, Sherry Chin, Ping Li, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Skeletal muscle fiber-type switching, exercise intolerance, and myopathy in PGC-1alpha muscle-specific knock-out animals."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M704817200"}], "href": "https://doi.org/10.1074/jbc.M704817200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17702743"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17702743"}]}, {"type": "r", "ref": 26, "children": [{"type": "t", "text": "Christoph Handschin, Cheol Soo Choi, Sherry Chin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Abnormal glucose homeostasis in skeletal muscle-specific PGC-1alpha knockout mice reveals skeletal muscle-pancreatic beta cell crosstalk."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Clin Invest (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1172/JCI31785"}], "href": "https://doi.org/10.1172/JCI31785"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17932564"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17932564"}]}, {"type": "r", "ref": 27, "children": [{"type": "t", "text": "John T Cunningham, Joseph T Rodgers, Daniel H Arlow, et al. "}, {"type": "b", "children": [{"type": "t", "text": "mTOR controls mitochondrial oxidative function through a YY1-PGC-1alpha transcriptional complex."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature06322"}], "href": "https://doi.org/10.1038/nature06322"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18046414"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18046414"}]}, {"type": "r", "ref": 28, "children": [{"type": "t", "text": "Jennifer A Calvo, Thomas G Daniels, Xiaomei Wang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Muscle-specific expression of PPARgamma coactivator-1alpha improves exercise performance and increases peak oxygen uptake."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Appl Physiol (1985) (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1152/japplphysiol.01231.2007"}], "href": "https://doi.org/10.1152/japplphysiol.01231.2007"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18239076"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18239076"}]}, {"type": "r", "ref": 29, "children": [{"type": "t", "text": "Zoltan Arany, Shi-Yin Foo, Yanhong Ma, et al. "}, {"type": "b", "children": [{"type": "t", "text": "HIF-independent regulation of VEGF and angiogenesis by the transcriptional coactivator PGC-1alpha."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature06613"}], "href": "https://doi.org/10.1038/nature06613"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18288196"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18288196"}]}, {"type": "r", "ref": 30, "children": [{"type": "t", "text": "Matthew J Potthoff, Takeshi Inagaki, Santhosh Satapati, et al. "}, {"type": "b", "children": [{"type": "t", "text": "FGF21 induces PGC-1alpha and regulates carbohydrate and fatty acid metabolism during the adaptive starvation response."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.0904187106"}], "href": "https://doi.org/10.1073/pnas.0904187106"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19541642"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19541642"}]}, {"type": "r", "ref": 31, "children": [{"type": "t", "text": "Jessica Chinsomboon, Jorge Ruas, Rana K Gupta, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The transcriptional coactivator PGC-1alpha mediates exercise-induced angiogenesis in skeletal muscle."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.0909131106"}], "href": "https://doi.org/10.1073/pnas.0909131106"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19966219"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19966219"}]}, {"type": "r", "ref": 32, "children": [{"type": "t", "text": "Orsolya M Palacios, Juan J Carmona, Shaday Michan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Diet and exercise signals regulate SIRT3 and activate AMPK and PGC-1alpha in skeletal muscle."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Aging (Albany NY) (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.18632/aging.100075"}], "href": "https://doi.org/10.18632/aging.100075"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20157566"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20157566"}]}, {"type": "r", "ref": 33, "children": [{"type": "t", "text": "Masato Iwabu, Toshimasa Yamauchi, Miki Okada-Iwabu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Adiponectin and AdipoR1 regulate PGC-1alpha and mitochondria by Ca(2+) and AMPK/SIRT1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature08991"}], "href": "https://doi.org/10.1038/nature08991"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20357764"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20357764"}]}, {"type": "r", "ref": 34, "children": [{"type": "t", "text": "Xingxing Kong, Rui Wang, Yuan Xue, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Sirtuin 3, a new target of PGC-1alpha, plays an important role in the suppression of ROS and mitochondrial biogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS One (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pone.0011707"}], "href": "https://doi.org/10.1371/journal.pone.0011707"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20661474"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20661474"}]}, {"type": "r", "ref": 35, "children": [{"type": "t", "text": "Mei Tran, Denise Tam, Amit Bardia, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PGC-1α promotes recovery after acute kidney injury during systemic inflammation in mice."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Clin Invest (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1172/JCI58662"}], "href": "https://doi.org/10.1172/JCI58662"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21881206"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21881206"}]}, {"type": "r", "ref": 36, "children": [{"type": "t", "text": "Pontus Boström, Jun Wu, Mark P Jedrychowski, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A PGC1-α-dependent myokine that drives brown-fat-like development of white fat and thermogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature10777"}], "href": "https://doi.org/10.1038/nature10777"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22237023"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22237023"}]}, {"type": "r", "ref": 37, "children": [{"type": "t", "text": "Taiji Tsunemi, Travis D Ashe, Bradley E Morrison, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PGC-1α rescues Huntington's disease proteotoxicity by preventing oxidative stress and promoting TFEB function."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Transl Med (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1126/scitranslmed.3003799"}], "href": "https://doi.org/10.1126/scitranslmed.3003799"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22786682"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22786682"}]}, {"type": "r", "ref": 38, "children": [{"type": "t", "text": "Jorge L Ruas, James P White, Rajesh R Rao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A PGC-1α isoform induced by resistance training regulates skeletal muscle hypertrophy."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2012.10.050"}], "href": "https://doi.org/10.1016/j.cell.2012.10.050"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23217713"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23217713"}]}, {"type": "r", "ref": 39, "children": [{"type": "t", "text": "Christiane D Wrann, James P White, John Salogiannnis, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Exercise induces hippocampal BDNF through a PGC-1α/FNDC5 pathway."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Metab (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cmet.2013.09.008"}], "href": "https://doi.org/10.1016/j.cmet.2013.09.008"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24120943"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24120943"}]}, {"type": "r", "ref": 40, "children": [{"type": "t", "text": "Leandro Z Agudelo, Teresa Femenía, Funda Orhan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Skeletal muscle PGC-1α1 modulates kynurenine metabolism and mediates resilience to stress-induced depression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2014.07.051"}], "href": "https://doi.org/10.1016/j.cell.2014.07.051"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25259918"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25259918"}]}, {"type": "r", "ref": 41, "children": [{"type": "t", "text": "Mei T Tran, Zsuzsanna K Zsengeller, Anders H Berg, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PGC1α drives NAD biosynthesis linking oxidative metabolism to renal protection."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature17184"}], "href": "https://doi.org/10.1038/nature17184"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26982719"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26982719"}]}, {"type": "r", "ref": 42, "children": [{"type": "t", "text": "Bertram Bengsch, Andy L Johnson, Makoto Kurachi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Bioenergetic Insufficiencies Due to Metabolic Alterations Regulated by the Inhibitory Receptor PD-1 Are an Early Driver of CD8(+) T Cell Exhaustion."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Immunity (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.immuni.2016.07.008"}], "href": "https://doi.org/10.1016/j.immuni.2016.07.008"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27496729"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27496729"}]}, {"type": "r", "ref": 43, "children": [{"type": "t", "text": "Nicole E Scharping, Ashley V Menk, Rebecca S Moreci, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The Tumor Microenvironment Represses T Cell Mitochondrial Biogenesis to Drive Intratumoral T Cell Metabolic Insufficiency and Dysfunction."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Immunity (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.immuni.2016.07.009"}], "href": "https://doi.org/10.1016/j.immuni.2016.07.009"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27496732"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27496732"}]}, {"type": "r", "ref": 44, "children": [{"type": "t", "text": "Rebecca C Rabinovitch, Bozena Samborska, Brandon Faubert, et al. "}, {"type": "b", "children": [{"type": "t", "text": "AMPK Maintains Cellular Metabolic Homeostasis through Regulation of Mitochondrial Reactive Oxygen Species."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Rep (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.celrep.2017.09.026"}], "href": "https://doi.org/10.1016/j.celrep.2017.09.026"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28978464"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28978464"}]}]}]}
Synonyms	SEMA-Z2, COLL-2
Proteins	SEM3D_HUMAN
NCBI Gene ID	223117
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

SEMA3D has 4,793 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 109 datasets.

Click the + buttons to view associations for SEMA3D from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

SEMA3D Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by SEMA3D gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of SEMA3D gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of SEMA3D gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of SEMA3D gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of SEMA3D gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of SEMA3D gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of SEMA3D gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of SEMA3D gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of SEMA3D gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of SEMA3D gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of SEMA3D gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of SEMA3D gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with SEMA3D gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of SEMA3D gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of SEMA3D gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of SEMA3D gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of SEMA3D gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing SEMA3D protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with SEMA3D protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with SEMA3D protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of SEMA3D gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with SEMA3D gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Disease Associations	diseases associated with SEMA3D gene/protein from the curated CTD Gene-Disease Associations dataset.
	dbGAP Gene-Trait Associations	traits associated with SEMA3D gene in GWAS and other genetic association datasets from the dbGAP Gene-Trait Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by SEMA3D gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores 2025	diseases involving SEMA3D gene from the DISEASES Curated Gene-Disease Association Evidence Scores 2025 dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores	diseases associated with SEMA3D gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with SEMA3D gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with SEMA3D gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with SEMA3D gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with SEMA3D gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with SEMA3D gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at SEMA3D gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of SEMA3D gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of SEMA3D gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing SEMA3D from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with SEMA3D gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with SEMA3D gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of SEMA3D gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with SEMA3D gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.