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Frequently Asked Questions (FAQs)Human Gene Expression Endometrial Receptivity Database (HGEx-ERdb) is a curated database of gene expression studies. It is created primarily to identify the genes which are expressed or repressed in the receptive or the mid secretory phase of human menstrual cycle. HGEx-ERdb provides the information on the endometrial expression of any gene of interest in other phases of menstrual cycle also. It is important to know which genes are expressed during the mid-secretory phase or the receptive phase of the endometrium as only during this phase, the endometrium becomes permissive to embryo implantation. The data has been compiled from Gene Expression Omnibus and peer reviewed journals. Human Gene Expression Endometrial Receptivity Database (HGEx-ERdb) can be queried for the expression status (upregulated/downregulated or transcribed/dormant) of the gene of interest or for a list of all the genes, reported to be expressed in endometrium during a specific phase (proliferative, secretory or menstrual) of human menstrual cycle. It allots a reliability score to the genes, depending on the consensus of their expression pattern across various investigations. HGEx-ERdb thus provides a bird’s eye-view of the identity and relative expression level of the genes expressed during the receptive phase in endometrium. Mozilla Firefox 3.0 or Internet Explorer 8.0 is preferred browser for faster results, although it works well with other browsers also. You are requested to enable javascript in your browser. Data can be downloaded by sending a request to Dr K. Acharya at kshitish@ibab.ac.in. This is the first half of the menstrual cycle and during this period, the endometrium grows under the influence of estrogen secreted by the ovary. During this phase the endometrium becomes dense and vascular. This phase also called as "follicular phase", spans days 5-14 of the menstrual cycle. Proliferative phase has been subdivided into early proliferative (day 5-9), mid proliferative (day 10-12) and late proliferative phase (day 13-14). Endometrial samples obtained during this phase of the menstrual cycle are referred to as "proliferative phase" samples in the database. This is the second half of menstrual cycle (days 15-28) and begins after the release of an ovum from the ovary. During this period the endometrium becomes thick and spongy due to development of glands and arteries under the influence of progesterone, secreted by the ruptured ovarian follicle. LH refers to the day of Leutinizing Hormone Surge (LH surge) and signifies the release of an ovum from the follicle. On the basis of the days elapsed after LH surge, proliferative phase has further been subdivided into three stages: early secretory (day 15-18 or LH +1-4 i.e. from day 1-4 post LH surge), mid secretory (day 19-23 or LH +5-9), late secretory (day 24-28 or LH +10-14) of the cycle. Endometrial samples obtained during this phase of the menstrual cycle are referred to as "secretory phase" samples in the database. This is the phase of the menstrual cycle during which the endometrial lining is shed off due to decline in progesterone levels. It lasts for four days and spans day 1-4 of the menstrual cycle. Endometrial samples obtained during this phase of the menstrual cycle are referred to as "menstrual phase" samples in the database. Endometrial samples obtained from women treated with either Follicle Stimulating Hormone (FSH) or hCG (Human Chorionic Gonadotropin) or both, have been grouped under "Hormone Treatment". FSH is used to stimulate the ovary to produce more than one egg, in women who opt for in vitro fertilization. FSH is usually combined with another drug (agonist or antagonist) to prevent the ovary from premature ovulation. When the follicles are mature, as indicated by their size and estrogen levels, ovulation is triggered using hCG or agonist. In Vitro Fertilization (IVF) is a type of assisted reproductive technique, in which the eggs from the women’s ovary are removed, fertilized with the sperm in appropriate laboratory conditions and the embryo is returned to the women’s uterus for further growth and development. ICSI or Intra Cytoplasmic Sperm Injection involves injection of a single sperm directly into an egg. This procedure is usually adopted to circumvent male infertility. Controlled Ovarian Stimulation/ Hyperstimulation Cycle (COS) is a part of IVF and involves monitored administration of ovulation inducing agents to increase the number of eggs released from the ovary and hence the probability of an egg being fertilized. Endometrial samples obtained from women who have been administered with the agents for hyperstimulation are referred to as "COS" cycle samples in the database. A gonadotropin-releasing hormone (GnRH) agonist is a synthetic peptide modeled after the hypothalamic neurohormone. It interacts with the gonadotropin-releasing hormone receptor (GnRHR) to elicit the release of the pituitary hormones i.e. Follicle Stimulating Hormone (FSH) and Leutinizing Hormone (LH). Women of reproductive age are treated with GnRH agonists to reduce the risk of oocyte loss and preserve ovarian function. Endometrial samples obtained from women who have been administered GnRH agonist for hyperstimulation are referred to as "GnRH agonist treatment" samples in the database. Gonadotropin-releasing hormone (GnRH) antagonists (receptor blockers) are a class of synthetic peptides that are similar in structure to natural GnRH but have an antagonistic effect. GnRH antagonists compete with natural GnRH for binding to GnRH receptors and thus decrease or block GnRH action. GnRH antagonists are also used for short periods to prevent premature leutinizing hormone (LH) surge and endogenous ovulation in patients undergoing exogenous stimulation with FSH in the preparation for IVF. GnRH antagonists are often administered in the mid-follicular phase in the stimulated cycles after administration of gonadotropins and prior to the administration of ovulation inducing agents. Endometrial samples obtained from women who have been administered with GnRH antagonist for hyperstimulation are referred to as "GnRH antagonist treatment" samples in the database. "Normal" refers to an endometrial sample obtained from a study participant with no known pathological condition. "Apparently normal" refers to a condition where the endometrium appears to be histologically normal but its donor has either undergone a surgery for medical problems not related to uterus, or currently has a disorder of extrauterine origin. These surgeries or extrauterine disorders are not expected to affect the endometrial tissue but in order to keep the "normal" group unadulterated, the samples are referred to as "apparently normal" samples. "Control" refers to endometrial tissue (primary tissue/cell line) treated with vehicle or DNA vector without the gene of interest or control siRNA. Studies based on the endometrial samples which do not fall under normal, apparently normal, chemical treatment, hormone treatment, or pathological condition” are grouped under "others". Endometrial cells/tissue propagated in media supplemented with exogenously added specific component (such as embryo secreted products) are grouped under "conditioned medium". Endometrial samples obtained from the tissues of women who have undergone Assisted Reproductive Technologies (ART), either in the same or previous menstrual cycle, are grouped under "ART outcome" (e.g. IVF, ICSI). Endometrial samples collected from women having a disorder of uterine or extra-uterine origin are grouped under "pathological condition". Endometrial samples obtained from the patients who have undergone a surgery for the disorders of extra-uterine origin in the past are grouped under "surgery". "Gene specific study" is assigned to those studies where the expression profiling is carried out in response to either overexpression or inhibition of a specific gene in endometrial tissue/cells/cell line. Contraception (birth control) is an approach designed to interfere with either ovulation or fertilization or implantation to prevent pregnancy. Hormonal methods, barrier methods, spermicides, intrauterine devices, tubal sterilization are some of the ways for contraception. Endometrial samples obtained from women who are using any of the contraceptive methods are referred to as "contraception" samples in the database. Gestation means pregnancy. Endometrial samples from pregnant women are grouped under "Gestation". The database structure is hierarchal. A list of genes along with their 'reliability score' can be obtained for the condition(s) of interest. On the other hand, the database can also be queried for expression status of the gene of interest across the menstrual cycle. A 'reliability-score' for each gene, is derived by the extent of agreement or contradiction on the expression pattern (up or down regulated, transcribed or dormant) across the comparable data sets in all studies. Higher the consensus, higher is the reliability score. The output displays the expression status of the gene of interest in human endometrium in a specific phase of menstrual cycle or in a specific condition; either in isolation (single status) or in comparison to other conditions (differential status). For a single status, the data can be obtained as a list of genes which display expression status either as transcribed or dormant, in a single condition specified by the user. This data is referred to as set 1. Data retrieved similarly for another condition is referred to as set 2. Differential status would yield information on the genes which are differentially expressed in set1 and set 2.The output genelist also has the option of displaying biological processes, molecular function and cellular components for each gene. Data source of the result can be accessed by selecting the references icon. The data have been categorized hierarchically (as indicated in the following figure) on the basis of phases of the menstrual cycle and also on the basis of the conditions to which endometrial samples have been subjected. The single and/or differential status of gene expression can be obtained by querying for any two sets of conditions and / or phases of the menstrual cycle. The two sets have been demonstrated in different colours in the figure. 
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