GO-ID	Process	Definition
	mobilization	HSCs move from the bone marrow to the peripheral blood, opposite to homing
	homing	HSCs move from the peripheral blood to the bone marrow, opposite to mobilization
	repopulation >16 weeks	successful engraftment (multilineage reconstitution) of HSCs for longer than 16 weeks, long-term reconstitution
	repopulation >32 weeks	successful engraftment (multilineage reconstitution) of HSCs for longer than 32 weeks, long-term reconstitution
	repopulation <12 weeks	successful engraftment (multilineage reconstitution) of HSCs for shorter than 12 weeks, short-term reconstitution
	repopulation, myeloid-biased	successful engraftment (multilineage reconstitution) of HSCs for longer than 16 weeks, but the number of myeloid cells is higher than the number of lymphoid cells
	repopulation, lymphoid-biased	successful engraftment (multilineage reconstitution) of HSCs for longer than 16 weeks, but the number of lymphoid cells is higher than the number of myeloid cells
	BM homeostasis	bone marrow cells are in a steady state condition, opposite to BM injury
	BM injury	opposite to bone marrow homeostasis
	TPO/MPL signaling	A series of molecular signals initiated by the binding of the extracellular ligand TPO (Thpo) to the receptor MPL on the surface of a target cell.
	Cxcl12/Cxcr4 signaling	A series of molecular signals initiated by the binding of the extracellular ligand Cxcl12 to the receptor Cxcr4 on the surface of a target cell.
	Tie2/Ang1 signaling	A series of molecular signals initiated by the binding of the extracellular ligand Ang1 (Angpt1) to the receptor Tie2 (Tek) on the surface of a target cell
	PI3K/AKT signaling	Akt (Akt1) phosphorylates Pi3k complex
	PTH signaling	PTH/PTHrP signaling pathway
	Erk signaling	Protein kinase signaling pathway
	Il7 response	Binding of interleukin-7 to a receptor initiating a series of molecular signals.
	cobblestone formation	experimentally verified extrinsic activity of a gene, activity of genes expressed in non-hematopoietic tissue
	non-cell autonomous activity	coculture of HSCs with stromal cells, HSCs crawl beneath the stromal cells to form "cobblestone areas"
GO:0000075	cell cycle checkpoint	A cell cycle process that controls cell cycle progression by monitoring the integrity of specific cell cycle events. A cell cycle checkpoint begins with detection of deficiencies or defects and ends with signal transduction.
GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
GO:0000723	telomere maintenance	Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins and the length of telomeric DNA. These processes includes those that shorten and lengthen the telomeric DNA sequences.
GO:0001503	ossification	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
GO:0001649	osteoblast differentiation	The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
GO:0001666	response to hypoxia	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
GO:0005921	gap junction	A cell-cell junction that is composed of an array of small channels that permit small molecules to pass from one cell to another. At gap junctions, the membranes of two adjacent cells are separated by a uniform narrow gap of about 2-4 nm that is spanned by channel-forming proteins called connexins, which form hexagonal tubes called connexons.
GO:0006306	DNA methylation	The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
GO:0006342	chromatin silencing	Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathways) which typically lead to rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. The process ends when the cell has died. The process is divided into a signaling pathway phase, and an execution phase, which is triggered by the former.
GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
GO:0007179	transforming growth factor beta receptor signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
GO:0007219	Notch signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
GO:0007224	smoothened signaling pathway	A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
GO:0007249	I-kappaB kinase/NF-kappaB cascade	The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
GO:0007259	JAK-STAT cascade	Any process in which STAT proteins (Signal Transducers and Activators of Transcription) and JAK (Janus Activated Kinase) proteins convey a signal to trigger a change in the activity or state of a cell. The JAK-STAT cascade begins with activation of STAT proteins by members of the JAK family of tyrosine kinases, proceeds through dimerization and subsequent nuclear translocation of STAT proteins, and ends with regulation of target gene expression by STAT proteins.
GO:0007265	Ras protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death (GO:0016265) and may succeed developmental maturation (GO:0021700).
GO:0009299	mRNA transcription	The cellular synthesis of messenger RNA (mRNA) from a DNA template.
GO:0016055	Wnt receptor signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
GO:0016477	cell migration	The orderly movement of a cell from one site to another, often during the development of a multicellular organism or multicellular structure. Used here to describe the movement of HSCs in in vitro assays.
GO:0016568	chromatin modification	The alteration of DNA, protein, or sometimes RNA, in chromatin, which may result in changing the chromatin structure.
GO:0016571	histone methylation	The modification of histones by addition of methyl groups.
GO:0016574	histone ubiquitination	The modification of histones by addition of ubiquitin groups.
GO:0017145	self-renwal, stem cell division	The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types.
GO:0030099	myeloid cell differentiation	The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
GO:0002320	lymphoid progenitor cell differentiation	The process in which a precursor cell type acquires the specialized features of a lymphoid progenitor cell. Lymphoid progenitor cells include progenitor cells for any of the lymphoid lineages.
GO:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
GO:0030217	T cell differentiation	The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
GO:0030218	erythrocyte differentiation	The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
GO:0030851	granulocyte differentiation	The process in which a myeloid precursor cell acquires specializes features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils.
GO:0030219	megakaryocyte differentiation	The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte.
GO:0030509	BMP signaling pathway	A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
GO:0035567	non-canonical Wnt receptor signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via effectors other than beta-catenin.
GO:0040029	regulation of gene expression, epigenetic	Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence.
GO:0042110	T cell activation	The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
GO:0042769	DNA damage response, detection of DNA damage	The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal.
GO:0043161	proteasomal ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
GO:0043491	protein kinase B signaling cascade	A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase B, which occurs as a result of a single trigger reaction or compound.
GO:0044027	hypermethylation of CpG island	An increase in the epigenetic methylation of cytosine and adenosine residues in a CpG island in DNA. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes.
GO:0045444	fat cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat.
GO:0055074	calcium ion homeostasis	Any process involved in the maintenance of an internal steady state of calcium ions within an organism or cell.
GO:0060070	canonical Wnt receptor signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
GO:0060218	hematopoietic stem cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a hematopoietic stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
GO:0060395	SMAD protein signal transduction	The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.
GO:0070317	quiescence, negative regulation of G0 to G1 transition	A cell cycle process that stops, prevents, or reduces the rate or extent of the transition from the G0 quiescent state to the G1 phase.
GO:0071666	Slit-Robo signaling complex	A protein-carbohydrate complex that consists of a transmembrane roundabout (Robo) receptor, an extracellular Slit ligand and heparin/heparan sulfate.