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vesicle-mediated transport

The directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell.

transport

The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells, or within a multicellular organism.

biological_process

Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

cellular process

Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.

intracellular transport

The directed movement of substances within a cell.

Golgi vesicle transport

The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles.

localization

Any process by which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in a specific location.

establishment of localization

The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.

cellular localization

Any process by which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within or in the membrane of a cell.

establishment of localization in cell

The directed movement of a substance or cellular entity, such as a protein complex or organelle, to a specific location within, or in the membrane of, a cell.

all

This term is the most general term possible

establishment of localization

The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.

cellular localization

Any process by which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within or in the membrane of a cell.

establishment of localization in cell

The directed movement of a substance or cellular entity, such as a protein complex or organelle, to a specific location within, or in the membrane of, a cell.

vesicle-mediated transport

The directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell.

intracellular transport

The directed movement of substances within a cell.

Golgi vesicle transport

The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles.

intracellular

The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

cellular_component

The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

cell

The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

cytoplasm

All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

cytoplasmic membrane-bounded vesicle

A membrane-bounded vesicle found in the cytoplasm of the cell.

cytoplasmic vesicle

A vesicle formed of membrane or protein, found in the cytoplasm of a cell.

vesicle

Any small, fluid-filled, spherical organelle enclosed by membrane or protein.

membrane-bounded vesicle

Any small, fluid-filled, spherical organelle enclosed by a lipid bilayer.

melanosome

A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.

organelle

Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.

membrane-bounded organelle

Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

intracellular organelle

Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.

intracellular membrane-bounded organelle

Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

intracellular part

Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

cytoplasmic part

Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

cell part

Any constituent part of a cell, the basic structural and functional unit of all organisms.

pigment granule

A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes.

all

This term is the most general term possible

cell part

Any constituent part of a cell, the basic structural and functional unit of all organisms.

cytoplasmic vesicle

A vesicle formed of membrane or protein, found in the cytoplasm of a cell.

intracellular membrane-bounded organelle

Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

intracellular part

Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

intracellular organelle

Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.

cytoplasmic membrane-bounded vesicle

A membrane-bounded vesicle found in the cytoplasm of the cell.

cytoplasmic membrane-bounded vesicle

A membrane-bounded vesicle found in the cytoplasm of the cell.

cytoplasmic part

Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

cytoplasmic vesicle

A vesicle formed of membrane or protein, found in the cytoplasm of a cell.

molecular_function

Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.

catalytic activity

Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

protein kinase activity

Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.

protein serine/threonine kinase activity

Catalysis of the reaction: ATP + a protein serine/threonine = ADP + protein serine/threonine phosphate.

receptor signaling protein serine/threonine kinase activity

NA

signal transducer activity

Mediates the transfer of a signal from the outside to the inside of a cell by means other than the introduction of the signal molecule itself into the cell.

receptor signaling protein activity

NA

kinase activity

Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.

transferase activity

Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.

transferase activity, transferring phosphorus-containing groups

Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).

phosphotransferase activity, alcohol group as acceptor

Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).

molecular transducer activity

The molecular function that accepts an input of one form and creates an output of a different form.

all

This term is the most general term possible

protein kinase activity

Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.

receptor signaling protein serine/threonine kinase activity

NA

Id	Pvalue	ExpCount	Count	Size	Term
GO:0016192	2.489e-03	3.305	13 ARF1, COPA, EXOC5, LMAN1, PICALM, RAB5A, RAB5C, SCAMP1, SNAP23, TGFBR2, TMED2, VAMP3, YIPF5	355	vesicle-mediated transport
GO:0048193	6.401e-03	0.689	6 ARF1, COPA, EXOC5, LMAN1, SCAMP1, SNAP23	74	Golgi vesicle transport
GO:0006901	1.684e-02	0.121	3 ARF1, COPA, PICALM	13	vesicle coating
GO:0006892	2.009e-02	0.1304	3 EXOC5, SCAMP1, SNAP23	14	post-Golgi vesicle-mediated transport
GO:0006900	2.009e-02	0.1304	3 ARF1, COPA, PICALM	14	membrane budding
GO:0015031	2.095e-02	4.897	14 ARF1, CANX, COPA, EXOC5, KPNA4, LMAN1, RAB5A, RAB5C, RANBP2, SCAMP1, SNAP23, TMED2, YIPF5, YWHAZ	526	protein transport
GO:0045184	2.125e-02	4.907	14 ARF1, CANX, COPA, EXOC5, KPNA4, LMAN1, RAB5A, RAB5C, RANBP2, SCAMP1, SNAP23, TMED2, YIPF5, YWHAZ	527	establishment of protein localization
GO:0016044	2.155e-02	2.179	9 ARF1, COPA, HSPA4, PICALM, RAB5A, RAB5C, SNAP23, TGFBR2, VAMP3	234	membrane organization
GO:0051656	2.536e-02	0.3445	4 ARF1, COPA, PAFAH1B1, SNAP23	37	establishment of organelle localization
GO:0006903	3.108e-02	0.1583	3 ARF1, COPA, SNAP23	17	vesicle targeting
GO:0051640	4.023e-02	0.4097	4 ARF1, COPA, PAFAH1B1, SNAP23	44	organelle localization
GO:0008104	4.162e-02	5.4	14 ARF1, CANX, COPA, EXOC5, KPNA4, LMAN1, RAB5A, RAB5C, RANBP2, SCAMP1, SNAP23, TMED2, YIPF5, YWHAZ	580	protein localization
GO:0048583	4.599e-02	1.127	6 ADAM10, FKBP1A, MAP3K7, MAPK1, OSMR, TGFBR2	121	regulation of response to stimulus
GO:0051650	4.763e-02	0.1955	3 ARF1, COPA, SNAP23	21	establishment of vesicle localization

Id	Pvalue	ExpCount	Count	Size	Term
GO:0031410	3.357e-06	3.062	16 ADAM10, CALU, CANX, CLIC4, COPA, FN1, GNA13, LAMP1, PICALM, RAB5A, RAB5C, SPAG9, SYPL1, TMED2, YIPF5, YWHAZ	319	cytoplasmic vesicle
GO:0031982	4.632e-06	3.139	16 ADAM10, CALU, CANX, CLIC4, COPA, FN1, GNA13, LAMP1, PICALM, RAB5A, RAB5C, SPAG9, SYPL1, TMED2, YIPF5, YWHAZ	327	vesicle
GO:0042470	4.170e-05	0.7391	8 CALU, CANX, GNA13, LAMP1, RAB5A, RAB5C, SYPL1, YWHAZ	77	melanosome
GO:0048770	4.170e-05	0.7391	8 CALU, CANX, GNA13, LAMP1, RAB5A, RAB5C, SYPL1, YWHAZ	77	pigment granule
GO:0016023	2.919e-04	2.476	12 ADAM10, CALU, CANX, FN1, GNA13, LAMP1, RAB5A, RAB5C, SPAG9, SYPL1, TMED2, YWHAZ	258	cytoplasmic membrane-bounded vesicle
GO:0031988	3.363e-04	2.515	12 ADAM10, CALU, CANX, FN1, GNA13, LAMP1, RAB5A, RAB5C, SPAG9, SYPL1, TMED2, YWHAZ	262	membrane-bounded vesicle
GO:0044444	7.234e-03	26.61	42 ACLY, ADAM10, ARF1, ATP6V1A, CALU, CANX, CD44, CLIC4, COPA, CYP51A1, DHX9, EPB41L2, ERLIN1, FKBP1A, FN1, GNA13, GNS, LAMP1, LMAN1, MAP3K7, MAP3K7IP2, MAPK1, MAPKAPK2, PAFAH1B1, PHTF2, PICALM, PIP5K1A, PSEN1, RAB5A, RAB5C, RANBP2, SCARB2, SEPT11, SMEK1, SPAG9, STIP1, SYPL1, TGFBR2, TMED2, UBXN4, YIPF5, YWHAZ	2772	cytoplasmic part
GO:0016020	2.083e-02	29.91	44 ADAM10, ARF1, ATP13A3, ATP6V1A, C19orf6, CANX, CAPRIN1, CD44, CLIC4, COPA, CPD, CYP51A1, DDX3X, EPB41L2, ERLIN1, GNA13, KPNA4, LAMP1, LMAN1, MAP3K7IP2, NID1, NOTCH2, OSMR, PAFAH1B1, PCDHGA11, PCDHGA3, PICALM, PIP5K1A, PSEN1, PTPRO, PXN, RAB5A, RAB5C, RANBP2, SCAMP1, SCARB2, SNAP23, SPAG9, SYPL1, TGFBR2, TMED2, UBXN4, VAMP3, YIPF5	3116	membrane
GO:0005737	2.561e-02	42.56	56 ACLY, ADAM10, ARF1, ATP6V1A, C19orf6, CALU, CANX, CAPRIN1, CD44, CDV3, CLIC4, COPA, CYP51A1, DAPK3, DDX3X, DHX9, EPB41L2, ERLIN1, EXOC5, FKBP1A, FN1, GNA13, GNS, GTF2I, HIPK3, KPNA4, LAMP1, LMAN1, MAP3K2, MAP3K7, MAP3K7IP2, MAPK1, MAPKAPK2, MBNL2, PAFAH1B1, PHTF2, PICALM, PIP5K1A, PSEN1, PXN, RAB5A, RAB5C, RANBP2, SCARB2, SEPT11, SMEK1, SNAP23, SPAG9, STIP1, SYPL1, TGFBR2, TMED2, UBXN4, WDR1, YIPF5, YWHAZ	4434	cytoplasm
GO:0009986	3.325e-02	1.219	6 ADAM10, CD44, LAMP1, NOTCH2, PSEN1, TGFBR2	127	cell surface
GO:0012505	4.181e-02	7.227	16 ADAM10, ARF1, CANX, COPA, CYP51A1, ERLIN1, KPNA4, LMAN1, PAFAH1B1, PIP5K1A, PSEN1, RANBP2, SYPL1, TMED2, UBXN4, YIPF5	753	endomembrane system
GO:0030141	4.567e-02	0.5375	4 FN1, SPAG9, SYPL1, TMED2	56	secretory granule

Id	Pvalue	ExpCount	Count	Size	Term
GO:0004702	4.868e-03	0.3672	5 FKBP1A, MAP3K2, MAP3K7, MAPK1, TGFBR2	40	receptor signaling protein serine/threonine kinase activity
GO:0005515	3.748e-02	41.35	55 ACLY, ADAM10, ARF1, CAPRIN1, CBFB, CD44, CLIC4, COL6A1, COPA, DAPK3, DAZAP2, DDX3X, DHX9, EPB41L2, FKBP1A, FN1, GNA13, GNS, GTF2I, KPNA4, LMAN1, MAP3K2, MAP3K7, MAP3K7IP2, MAPK1, MAPKAPK2, MAT2A, MAX, NID1, NOTCH2, OSMR, PAFAH1B1, PCDHGA11, PCDHGA3, PICALM, PRPF4B, PRRX1, PSEN1, PTBP1, PXN, RAB5A, RAB5C, RANBP2, SCARB2, SEPT11, SMEK1, SNAP23, SPAG9, STIP1, TGFBR2, TMED2, UBXN4, WAC, WDR1, YWHAZ	4505	protein binding
GO:0005057	3.755e-02	0.9913	6 ARF1, FKBP1A, MAP3K2, MAP3K7, MAPK1, TGFBR2	108	receptor signaling protein activity
GO:0004674	4.937e-02	2.442	9 DAPK3, FKBP1A, HIPK3, MAP3K2, MAP3K7, MAPK1, MAPKAPK2, PRPF4B, TGFBR2	266	protein serine/threonine kinase activity

No enriched terms

Id	Pvalue	ExpCount	Count	Size
miR-320/320abcd	2.794e-03	4.794	19 ARF1, ATP13A3, ATP6V1A, CAPRIN1, CPD, GNS, HIPK3, HSPA4, LAMP1, MAPK1, MAT2A, MAX, PHTF2, RANBP2, SS18, TGFBR2, WDR1, YIPF5, YWHAZ	372

No enriched terms

Entrez genes

ACLYATP citrate lyase (210337_s_at), score: 0.78 ADAM10ADAM metallopeptidase domain 10 (214895_s_at), score: 0.7 ARF1ADP-ribosylation factor 1 (208750_s_at), score: 0.75 ATP13A3ATPase type 13A3 (219558_at), score: 0.81 ATP6V1AATPase, H+ transporting, lysosomal 70kDa, V1 subunit A (201971_s_at), score: 0.82 C19orf6chromosome 19 open reading frame 6 (213986_s_at), score: 0.82 CALUcalumenin (214845_s_at), score: 0.91 CANXcalnexin (208853_s_at), score: 0.82 CAPRIN1cell cycle associated protein 1 (200722_s_at), score: 0.7 CBFBcore-binding factor, beta subunit (206788_s_at), score: 0.7 CD44CD44 molecule (Indian blood group) (210916_s_at), score: 0.75 CDV3CDV3 homolog (mouse) (213548_s_at), score: 0.98 CLIC4chloride intracellular channel 4 (201559_s_at), score: 0.7 COL6A1collagen, type VI, alpha 1 (212940_at), score: 0.88 COPAcoatomer protein complex, subunit alpha (214336_s_at), score: 0.98 CPDcarboxypeptidase D (201942_s_at), score: 0.96 CYP51A1cytochrome P450, family 51, subfamily A, polypeptide 1 (216607_s_at), score: 0.83 DAPK3death-associated protein kinase 3 (203890_s_at), score: 0.69 DAZAP2DAZ associated protein 2 (212595_s_at), score: 0.79 DDX3XDEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked (201211_s_at), score: 1 DHX9DEAH (Asp-Glu-Ala-His) box polypeptide 9 (212105_s_at), score: 0.99 EPB41L2erythrocyte membrane protein band 4.1-like 2 (201718_s_at), score: 0.74 ERLIN1ER lipid raft associated 1 (202444_s_at), score: 0.74 EXOC5exocyst complex component 5 (218748_s_at), score: 0.76 FKBP1AFK506 binding protein 1A, 12kDa (210186_s_at), score: 0.81 FN1fibronectin 1 (214701_s_at), score: 0.86 GNA13guanine nucleotide binding protein (G protein), alpha 13 (206917_at), score: 0.74 GNSglucosamine (N-acetyl)-6-sulfatase (203676_at), score: 0.9 GTF2Igeneral transcription factor II, i (210892_s_at), score: 0.85 HIPK3homeodomain interacting protein kinase 3 (210148_at), score: 0.71 HSPA4heat shock 70kDa protein 4 (211016_x_at), score: 0.73 KPNA4karyopherin alpha 4 (importin alpha 3) (209653_at), score: 0.85 LAMP1lysosomal-associated membrane protein 1 (201551_s_at), score: 0.72 LMAN1lectin, mannose-binding, 1 (203294_s_at), score: 0.87 MAP3K2mitogen-activated protein kinase kinase kinase 2 (221695_s_at), score: 0.85 MAP3K7mitogen-activated protein kinase kinase kinase 7 (211537_x_at), score: 0.8 MAP3K7IP2mitogen-activated protein kinase kinase kinase 7 interacting protein 2 (210284_s_at), score: 0.86 MAPK1mitogen-activated protein kinase 1 (208351_s_at), score: 0.77 MAPKAPK2mitogen-activated protein kinase-activated protein kinase 2 (201461_s_at), score: 0.77 MAT2Amethionine adenosyltransferase II, alpha (200769_s_at), score: 0.94 MAXMYC associated factor X (210734_x_at), score: 0.89 MBNL2muscleblind-like 2 (Drosophila) (205018_s_at), score: 0.77 NID1nidogen 1 (202008_s_at), score: 0.73 NOTCH2Notch homolog 2 (Drosophila) (210756_s_at), score: 0.79 OSMRoncostatin M receptor (205729_at), score: 0.73 PAFAH1B1platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa (211547_s_at), score: 0.75 PCDHGA11protocadherin gamma subfamily A, 11 (211876_x_at), score: 0.96 PCDHGA3protocadherin gamma subfamily A, 3 (216352_x_at), score: 0.87 PHTF2putative homeodomain transcription factor 2 (217097_s_at), score: 0.88 PICALMphosphatidylinositol binding clathrin assembly protein (215236_s_at), score: 0.9 PIP5K1Aphosphatidylinositol-4-phosphate 5-kinase, type I, alpha (211205_x_at), score: 0.75 PRPF4BPRP4 pre-mRNA processing factor 4 homolog B (yeast) (211090_s_at), score: 0.79 PRRX1paired related homeobox 1 (205991_s_at), score: 0.91 PSEN1presenilin 1 (207782_s_at), score: 0.71 PTBP1polypyrimidine tract binding protein 1 (212016_s_at), score: 0.95 PTPROprotein tyrosine phosphatase, receptor type, O (211600_at), score: 0.76 PXNpaxillin (211823_s_at), score: 0.76 RAB5ARAB5A, member RAS oncogene family (206113_s_at), score: 0.99 RAB5CRAB5C, member RAS oncogene family (201156_s_at), score: 0.87 RANBP2RAN binding protein 2 (201711_x_at), score: 0.76 SCAMP1secretory carrier membrane protein 1 (206667_s_at), score: 0.81 SCARB2scavenger receptor class B, member 2 (201647_s_at), score: 0.72 SEPT11septin 11 (201308_s_at), score: 0.71 SMEK1SMEK homolog 1, suppressor of mek1 (Dictyostelium) (220368_s_at), score: 0.87 SNAP23synaptosomal-associated protein, 23kDa (214544_s_at), score: 0.74 SPAG9sperm associated antigen 9 (206748_s_at), score: 0.73 SS18synovial sarcoma translocation, chromosome 18 (216684_s_at), score: 0.72 STIP1stress-induced-phosphoprotein 1 (212009_s_at), score: 0.82 SYPL1synaptophysin-like 1 (201259_s_at), score: 0.85 TAF9BTAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa (221618_s_at), score: 0.72 TGFBR2transforming growth factor, beta receptor II (70/80kDa) (207334_s_at), score: 0.79 TMED2transmembrane emp24 domain trafficking protein 2 (204426_at), score: 0.76 UBXN4UBX domain protein 4 (212008_at), score: 0.77 VAMP3vesicle-associated membrane protein 3 (cellubrevin) (201337_s_at), score: 0.8 WACWW domain containing adaptor with coiled-coil (219679_s_at), score: 0.94 WDR1WD repeat domain 1 (210935_s_at), score: 0.69 YIPF5Yip1 domain family, member 5 (221423_s_at), score: 0.7 YWHAZtyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide (200641_s_at), score: 0.75

Non-Entrez genes

Unknown, score:

Id	sample	Experiment	ExpName	Array	Syndrome	Cell.line
ctrl c 08-03.CEL	3	1	DS-CC	hgu133a	none	DS-CC 3
E-TABM-263-raw-cel-1515486031.cel	20	6	Cycle	hgu133a2	none	Cycle 1
4Twin.CEL	4	2	DS-twin	hgu133plus2	none	DS-twin 4
1Twin.CEL	1	2	DS-twin	hgu133plus2	Down	DS-twin 1
E-GEOD-3407-raw-cel-1437949655.cel	3	4	Cockayne	hgu133a	none	CSB
E-GEOD-3407-raw-cel-1437949938.cel	8	4	Cockayne	hgu133a	none	CSB
E-GEOD-3407-raw-cel-1437949854.cel	7	4	Cockayne	hgu133a	CS	eGFP