BIO project GO-term table
Revision as of 20:18, 24 October 2015 by Boris (talk | contribs) (→How to use the table to adopt a function for the project)
GO term Table
Contents
Extracting Gene functions from GO and GOA
This table below of selected GO terms with human gene annotations in GOA is a starting point for function definition and gene selection.
Creation of the Function Table
The Function Table was created in the following steps:
- 1. I downloaded the file
gene_association.goa_humanfrom its GOA repository at the EBI. The file contains gene names and GO terms - here is an (abridged) example:
UniProtID GeneName GOtermID Description taxID A0A183 LCE6A GO:0031424 Late cornified envelope protein 6A taxon:9606
- 2. I downloaded the GO Ontologies file
go-basic.obofrom its repository at GO -the Gene Ontology Consortium. It contains the actual ontology terms, they look like this.
[Term] id: GO:0001776 name: leukocyte homeostasis namespace: biological_process def: "The process of regulating the proliferation and elimination of cells of the immune system such that the total number of cells of a particular cell type within a whole or part of an organism is stable over time in the absence of an outside stimulus." is_a: GO:0002376 ! immune system process is_a: GO:0048872 ! homeostasis of number of cells
- Note the two
is_arelationships that indicate the parent node, of which this one is a specialization.
- 3. I reconstructed the DAG (Directed Acyclic Graph) by connecting each of the 40,402 nodes to its parent node.
- 4. I eliminated all nodes that don't have at least one human gene in GOA annotated to it or one of its descendants. These are genes that might be specific to fungi, prokaryotes, viruses or similar.
- 5. For each node, I counted its distance from the root node. This "depth" tells us a bit about how specific a term is.
- 6. For each node, I counted how many human genes have been specifically annotated to it. This helps us a bit to indetify categories that are overly broad.
- 7. I wrote this information to file for the biological process ontology. The result has 11,927 nodes, one per line, and looks like this:
01 GO:0002376 immune system process [ ADSS ... 17 genes ] 05 GO:0001776 leukocyte homeostasis [MEN1, FLT3, NKX2-3] 06 GO:0001780 neutrophil homeostasis [ MECOM ... 13 genes ]
- Here, neutrophil homeostasis has 13 annotated genes, it is six steps removed from the root. Its parent is leukocyte homeostasis which itself is a specialization (a descendant) of an immune system process. The intermediate nodes are not shown because there are no genes directly annotated to these terms. Now consider what it means to find a gene at these levels:
MECOMis involved in the homeostasis (keeping cell-numbers constant) of neutrophil white blood cells.MEN1is also involved in white blood cell homeostasis, but it could either target several cell types, or it is not known which cell type it targets. Thus it is annotated to a higher node.ADSSseems to be a gene for which we know it is involved in the immune system, but we don't know what it does there. This illustrates how partial knowledge can be represented in this data structure, and you can easily imagine that, as we learn more about biology, we move annotations down to more precise locations, or create new nodes to represent new knowledge.
- 8. Next, I selected from this list. For this project we are looking for terms that give a good approximation of a cellular function, without being either too broad or too specialized. I selected nodes that have from 1 to 4 annotated genes at a depth between 2 and 5, and I excluded terms with keywords that indicate a role in a higher function of the organism such as "morphogenesis", "development" and "behavior". This yields 541 processes represented by 1,214 unique annotated genes.
- 9. To create the table you see below, I wrote the output in HTML table format to file, while adding links to the UniProt entry for the gene name. The gene names come from HGNC so I would expect all of the genes to be findable at UniProt.
How to use the table to adopt a function and define a "system" for the project
- I have randomly chosen a function and gone through the first stage of the project to illustrate the process
- 1. Browse the table and find a function that interests you. Its very diverse and will give you a good first sense of the complexity of functions in the cell and our state of knowledge about them.
- 2. Look at the function information available at UniProt. Most of these genes have more than one GO term annotated to them. For example I could choose (at random) SRPX, which plays a role in phagolysosome assembly. Here are the annotated processes in which this protein participates:
Just looking at these processes tells me a lot. The annotation is for one protein, but it is implied in several aspects of biology. Some of them are causal to others, and some of them are generalizations. Here, the phagolysosome needs to be assembled in order to function. Once it has been made, this enables stress response, and contact inhibition, likely via apoptotic pathways and autophagy. This phagolysosome assembly sounds like a good system to work on. But is the term too broad, or too narrow? Could I find a better name for it?
- 3. Follow the link to the phagolysosome assembly GOterm page at QuickGO, and explore the tabs that contain ancestral nodes and child nodes:
| Relationship to GO:0001845 |
Child Term | Child Term Name |
Part of |
GO:0090384 | phagosome-lysosome docking |
Part of |
GO:0090385 | phagosome-lysosome fusion |
Is a |
GO:0090387 | phagolysosome assembly involved in apoptotic cell clearance |
As a result of the exploration I see:
- There are 20 to 30 proteins annotated to this process;
- Most of them are not human, but from closely related species (e.g. baboon), that will probably allow inference from homology;
- If I set a filter to show only human proteins, I see that most of them are RAB genes which have a reasonably well understood functio. It will be interesting to find out how this function enables the process;
- The mechanism of this system will likely include proteins that are specific to this process, and others that are involved in membrane fusion in a general sense and are recruited to this specific task.
This actually looks like an ideal starting point to define the components of a system. For now, I would be oK with calling it the "Phagosome / Lysosome Fusion System".
What to submit for Part 1 of the project
- Head over to my 2015 project page on the student wiki.
- Copy the page content Wiki code and use it to create a subpage of your user space on the Student Wiki.
- Edit the page for your adopted system. Make sure the result contains all elements of the original (and none of the elements that are specific to me or the template project.
The Function Table
| Depth | GO Term | Text | Genes |
| 5 | GO:0001776 | leukocyte homeostasis | MEN1, FLT3, NKX2-3 |
| 3 | GO:0016445 | somatic diversification of immunoglobulins | AICDA, CTNNBL1, RAG2 |
| 5 | GO:0002366 | leukocyte activation involved in immune response | SH2D1B, CLEC7A, SYK |
| 5 | GO:0019724 | B cell mediated immunity | SLA2, MSH2, FAS |
| 4 | GO:0002679 | respiratory burst involved in defense response | NCF1, MPO, PIK3CG, PIK3CD |
| 5 | GO:0045728 | respiratory burst after phagocytosis | HCK, SELK |
| 3 | GO:0002352 | B cell negative selection | BAX, BAK1 |
| 4 | GO:0002367 | cytokine production involved in immune response | MR1, NOD2 |
| 3 | GO:0002377 | immunoglobulin production | FAS, IL7R |
| 4 | GO:0002381 | immunoglobulin production involved in immunoglobulin mediated immune response | HLA-DQB1, HLA-DRB1, NOD2 |
| 3 | GO:0002513 | tolerance induction to self antigen | LYN, FOXP3, TGFB1 |
| 4 | GO:0002384 | hepatic immune response | IL6, IL6R |
| 4 | GO:0002418 | immune response to tumor cell | PRF1, MICA |
| 3 | GO:0042092 | type 2 immune response | IL4, BCL6, IL18, IL10 |
| 4 | GO:0002495 | antigen processing and presentation of peptide antigen via MHC class II | MARCH1, MARCH8 |
| 2 | GO:0045058 | T cell selection | CD1D, CD4, CD74 |
| 3 | GO:0043366 | beta selection | ZAP70, SYK |
| 3 | GO:0043368 | positive T cell selection | THEMIS, BCL11B |
| 3 | GO:0045061 | thymic T cell selection | CARD11, JAG2, GATA3 |
| 5 | GO:0050902 | leukocyte adhesive activation | CX3CL1, SELPLG |
| 5 | GO:0018916 | nitrobenzene metabolic process | GSTM1, GSTM2, GSTM3 |
| 5 | GO:0006579 | amino-acid betaine catabolic process | BHMT, DMGDH |
| 5 | GO:0033076 | isoquinoline alkaloid metabolic process | CYP2D6, TH, DDC |
| 5 | GO:0000255 | allantoin metabolic process | STAT5B, STAT5A, GHR |
| 5 | GO:0009822 | alkaloid catabolic process | CYP2D6, CYP3A4, CYP3A5 |
| 5 | GO:0070458 | cellular detoxification of nitrogen compound | GSTM1, GSTM2, GSTM3 |
| 4 | GO:0051410 | detoxification of nitrogen compound | MARC1, MARC2 |
| 4 | GO:0009820 | alkaloid metabolic process | CYP2D6, CYP1A2 |
| 5 | GO:0042412 | taurine biosynthetic process | CDO1, CSAD |
| 2 | GO:0009056 | catabolic process | TMEM150A, CES2, PTER |
| 5 | GO:0042447 | hormone catabolic process | ECE1, ACE, IDE |
| 5 | GO:0044242 | cellular lipid catabolic process | ACADL, MT3 |
| 4 | GO:0046185 | aldehyde catabolic process | ALDH3B1, GPI, AKR1A1 |
| 5 | GO:0046294 | formaldehyde catabolic process | ESD, ADH5 |
| 5 | GO:0046952 | ketone body catabolic process | BDH1, ACAT1, OXCT1, OXCT2 |
| 5 | GO:0006706 | steroid catabolic process | STS, CYP1A2, HSD17B14, CYP3A4 |
| 5 | GO:0044240 | multicellular organismal lipid catabolic process | PLA2G1B, APOA4 |
| 5 | GO:0016139 | glycoside catabolic process | GBA2, GBA3, NAGA, GLA |
| 5 | GO:0000272 | polysaccharide catabolic process | CHIT1, CHIA |
| 4 | GO:0016052 | carbohydrate catabolic process | PGM2, PGM2L1, NAGA, AMY2A |
| 3 | GO:0010025 | wax biosynthetic process | FAR1, AWAT2 |
| 5 | GO:0070814 | hydrogen sulfide biosynthetic process | MPST, CBS, CTH |
| 5 | GO:0002378 | immunoglobulin biosynthetic process | GALNT2, PTPRC |
| 4 | GO:0006082 | organic acid metabolic process | CYP2C8, FMO2, FMO1 |
| 4 | GO:0015980 | energy derivation by oxidation of organic compounds | ACSM1, ACADVL |
| 4 | GO:0018894 | dibenzo-p-dioxin metabolic process | CYP1A2, CYP17A1, STAR, CYP11A1 |
| 4 | GO:0000103 | sulfate assimilation | SULT2B1, PAPSS1, PAPSS2 |
| 4 | GO:0019417 | sulfur oxidation | MICAL1, MICAL2 |
| 5 | GO:0030388 | fructose 1,6-bisphosphate metabolic process | PFKL, ALDOA, ALDOC, ALDOB |
| 5 | GO:0017143 | insecticide metabolic process | CYP1A1, STAR |
| 5 | GO:0052314 | phytoalexin metabolic process | TH, DDC |
| 4 | GO:0016999 | antibiotic metabolic process | TXN, DPEP1 |
| 4 | GO:0042133 | neurotransmitter metabolic process | GCHFR, CLN3, CACNA1A, AGTPBP1 |
| 4 | GO:0042180 | cellular ketone metabolic process | CYP2B6, DHRS4 |
| 5 | GO:1901661 | quinone metabolic process | CRYZL1, ADH4 |
| 5 | GO:0006643 | membrane lipid metabolic process | AGMO, B4GALT4 |
| 5 | GO:0006720 | isoprenoid metabolic process | PHYH, GGPS1 |
| 5 | GO:0046485 | ether lipid metabolic process | TMEM86B, AGMO, HRASLS |
| 3 | GO:0072592 | oxygen metabolic process | NOX1, ME3, FMO2 |
| 4 | GO:0042743 | hydrogen peroxide metabolic process | NOX1, PARK7 |
| 4 | GO:0005976 | polysaccharide metabolic process | CHST1, CHST7, TYMS |
| 5 | GO:0070085 | glycosylation | CLN5, COG6 |
| 5 | GO:0042982 | amyloid precursor protein metabolic process | KLK6, DLG1, LDLRAP1, ACHE |
| 5 | GO:1990000 | amyloid fibril formation | RIPK1, RIPK3 |
| 3 | GO:0044236 | multicellular organismal metabolic process | GHR, TIPARP, MNAT1 |
| 4 | GO:0044259 | multicellular organismal macromolecule metabolic process | TUB, AKR1C3 |
| 5 | GO:0002268 | follicular dendritic cell differentiation | BCL3, NFKB2 |
| 4 | GO:0014719 | satellite cell activation | WNT7A, MEGF10 |
| 4 | GO:0048143 | astrocyte activation | AGT, ADORA2A |
| 4 | GO:0072537 | fibroblast activation | RGCC, IL17A, IL17RA |
| 4 | GO:0016080 | synaptic vesicle targeting | NLGN1, SCRIB, PSEN1, SEPT5 |
| 5 | GO:0048203 | vesicle targeting, trans-Golgi to endosome | AP1AR, WIPI1 |
| 5 | GO:0030050 | vesicle transport along actin filament | FNBP1L, WASL |
| 5 | GO:0031022 | nuclear migration along microfilament | SYNE2, SUN2 |
| 5 | GO:0070358 | actin polymerization-dependent cell motility | JMY, NCKAP1L, EPS8 |
| 5 | GO:0097491 | sympathetic neuron projection guidance | NRP1, NRP2, SEMA3A, SEMA3F |
| 3 | GO:0006949 | syncytium formation | ERCC1, CCNG1, ERVW-1 |
| 5 | GO:0006999 | nuclear pore organization | NUP98, SEH1L, NUP133, TPR |
| 5 | GO:0007000 | nucleolus organization | NOLC1, RRN3, RPS19, PES1 |
| 5 | GO:0007290 | spermatid nucleus elongation | TNP1, H1FNT, KDM3A |
| 5 | GO:0030382 | sperm mitochondrion organization | PVRL2, SEPT4 |
| 5 | GO:0090161 | Golgi ribbon formation | OPTN, TMED5, GCC2 |
| 5 | GO:0090166 | Golgi disassembly | PLK3, VRK1 |
| 4 | GO:0007033 | vacuole organization | MAN2A1, FIG4, NDP |
| 5 | GO:0006900 | membrane budding | P2RX7, FNBP1L, WASL |
| 5 | GO:0030719 | P granule organization | PLD6, TDRD5 |
| 4 | GO:0031023 | microtubule organizing center organization | PAFAH1B1, CLASP2, CLASP1, GCC2 |
| 5 | GO:0000715 | nucleotide-excision repair, DNA damage recognition | XPC, RAD23B |
| 5 | GO:0000819 | sister chromatid segregation | TOP2B, TOP2A, LATS1 |
| 5 | GO:0006344 | maintenance of chromatin silencing | HDAC2, UBE2B, SIRT1 |
| 5 | GO:0000022 | mitotic spindle elongation | PRC1, KIF23 |
| 5 | GO:0098535 | de novo centriole assembly | CCDC78, PLK4, CEP152, CCDC67 |
| 3 | GO:0007028 | cytoplasm organization | TFCP2L1, RRN3, KIF5B |
| 4 | GO:0007296 | vitellogenesis | ZMIZ1, FOSL1 |
| 5 | GO:0007113 | endomitotic cell cycle | UBA3, CIB1, PLK3 |
| 5 | GO:0007060 | male meiosis chromosome segregation | TEX11, MLH1 |
| 5 | GO:0045143 | homologous chromosome segregation | ESPL1, MSH4, MSH5 |
| 5 | GO:0021937 | cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation | LHX5, LHX1 |
| 5 | GO:0035425 | autocrine signaling | HILPDA, FZD1 |
| 5 | GO:0038001 | paracrine signaling | PDGFB, CD34 |
| 5 | GO:0060638 | mesenchymal-epithelial cell signaling | HOXA5, WNT5A, WNT2B |
| 5 | GO:0060684 | epithelial-mesenchymal cell signaling | WNT6, SMO, BMP4, CDC42 |
| 4 | GO:0007412 | axon target recognition | UCHL1, BDNF, FOXB1, STXBP1 |
| 4 | GO:0010643 | cell communication by chemical coupling | DBN1, GJA1 |
| 4 | GO:0010644 | cell communication by electrical coupling | DBN1, GJA1 |
| 5 | GO:0071460 | cellular response to cell-matrix adhesion | SKP2, DSPP |
| 4 | GO:0035426 | extracellular matrix-cell signaling | FZD4, FER, NDP |
| 5 | GO:0086067 | AV node cell to bundle of His cell communication | CXADR, SCN10A, SCN5A, SCN4B |
| 5 | GO:0086070 | SA node cell to atrial cardiac muscle cell communication | SCN3B, ANK2, SCN5A |
| 5 | GO:0006931 | substrate-dependent cell migration, cell attachment to substrate | EPB41L5, TNFRSF12A, CUZD1 |
| 5 | GO:0003365 | establishment of cell polarity involved in ameboidal cell migration | AMOTL1, AMOT |
| 5 | GO:0045200 | establishment of neuroblast polarity | DOCK7, FGF13, RAB10 |
| 4 | GO:0030011 | maintenance of cell polarity | DST, NCKAP1L, ATN1 |
| 5 | GO:0001300 | chronological cell aging | ENG, SERPINE1 |
| 5 | GO:0001302 | replicative cell aging | ERCC1, WRN, ROMO1 |
| 5 | GO:0043654 | recognition of apoptotic cell | JMJD6, PEAR1, SCARB1, MEGF10 |
| 5 | GO:0016198 | axon choice point recognition | GAP43, EFNB3 |
| 5 | GO:0070593 | dendrite self-avoidance | DSCAM, DSCAML1 |
| 4 | GO:0009988 | cell-cell recognition | CLEC4M, FUT3, CD209, ST6GALNAC6 |
| 5 | GO:0001771 | immunological synapse formation | DOCK2, CCL19, CCL21, DLG1 |
| 5 | GO:0070269 | pyroptosis | NLRC4, AIM2 |
| 5 | GO:0001555 | oocyte growth | KMT2D, GDF9 |
| 5 | GO:0070050 | neuron cellular homeostasis | CHRNA1, TYRO3, HAAO, FGGY |
| 5 | GO:0031577 | spindle checkpoint | SPDL1, BIRC5, TAOK1 |
| 4 | GO:0000320 | re-entry into mitotic cell cycle | GSK3B, CCNF, CCND1 |
| 5 | GO:0033206 | meiotic cytokinesis | ACTR3, ACTR2 |
| 4 | GO:0007127 | meiosis I | PSMD13, CKS2 |
| 5 | GO:0051322 | anaphase | CUL3, USP44 |
| 5 | GO:0007109 | cytokinesis, completion of separation | SPAST, ANXA11 |
| 5 | GO:0034088 | maintenance of mitotic sister chromatid cohesion | NIPBL, DSCC1, RB1, MAU2 |
| 4 | GO:0044770 | cell cycle phase transition | TIPIN, TIMELESS, CDC7, PTPRC |
| 4 | GO:0045023 | G0 to G1 transition | MDM4, CDK3 |
| 4 | GO:0051304 | chromosome separation | SMARCAD1, RECQL5 |
| 5 | GO:0051306 | mitotic sister chromatid separation | TEX14, DIS3L2 |
| 5 | GO:0051653 | spindle localization | ACTR3, ACTR2, WASL |
| 4 | GO:0070314 | G1 to G0 transition | EZH2, CYP27B1, C2orf40 |
| 5 | GO:0070315 | G1 to G0 transition involved in cell differentiation | SLC39A5, CAPN3 |
| 4 | GO:0048278 | vesicle docking | EXOC5, CAV2, CCDC41 |
| 5 | GO:0043241 | protein complex disassembly | DDIT4, HDAC6 |
| 3 | GO:0030029 | actin filament-based process | ELMO1, SELE |
| 5 | GO:0006930 | substrate-dependent cell migration, cell extension | OPHN1, SDCBP, MYH10, CD2AP |
| 5 | GO:0030035 | microspike assembly | ACTN2, FGD4, MTSS1 |
| 4 | GO:0032796 | uropod organization | CORO1A, MYH9 |
| 5 | GO:0044375 | regulation of peroxisome size | PEX11G, PEX11A, PEX11B |
| 4 | GO:0043482 | cellular pigment accumulation | SHROOM3, SHROOM2 |
| 5 | GO:0002934 | desmosome organization | DSP, PERP, PVRL1 |
| 3 | GO:0035845 | photoreceptor cell outer segment organization | AHI1, RP1, TOPORS, NPHP1 |
| 5 | GO:0071711 | basement membrane organization | FSHR, RIC8A, TFAP2A |
| 4 | GO:0097062 | dendritic spine maintenance | PICK1, TANC1, MTMR2 |
| 5 | GO:0007501 | mesodermal cell fate specification | HOXA11, EYA2, PAX2, SIX2 |
| 5 | GO:0048866 | stem cell fate specification | SOX18, SOX17 |
| 5 | GO:0007403 | glial cell fate determination | NTF3, CTNNB1, SMARCA4 |
| 5 | GO:0007493 | endodermal cell fate determination | SOX17, GATA6 |
| 5 | GO:0007500 | mesodermal cell fate determination | KLF4, BMP4, TRIM15, TDGF1P3 |
| 5 | GO:0007518 | myoblast fate determination | IFRD1, MYOD1 |
| 5 | GO:0007521 | muscle cell fate determination | TBX2, MEF2C, MEF2A |
| 5 | GO:0048664 | neuron fate determination | WNT1, LBX1, CDC42 |
| 5 | GO:0060913 | cardiac cell fate determination | MESP1, ISL1, POU5F1, SOX17 |
| 5 | GO:0001826 | inner cell mass cell differentiation | NLE1, TET1, HNF1B |
| 5 | GO:0009994 | oocyte differentiation | KMT2B, NPM2 |
| 5 | GO:0010668 | ectodermal cell differentiation | ERF, VPS52 |
| 5 | GO:0021533 | cell differentiation in hindbrain | PHOX2B, NOG, FOXA2, GATA2 |
| 5 | GO:0021979 | hypothalamus cell differentiation | OTP, POU3F2, PROP1 |
| 5 | GO:0035987 | endodermal cell differentiation | NODAL, HMGA2, MIXL1 |
| 5 | GO:0035990 | tendon cell differentiation | TNMD, BMP4, MKX, SCXA |
| 5 | GO:0048333 | mesodermal cell differentiation | HMGA2, KDM6A, INHBA |
| 5 | GO:0060126 | somatotropin secreting cell differentiation | WNT4, PITX2, PROP1 |
| 5 | GO:0060128 | corticotropin hormone secreting cell differentiation | FGF8, FGF2, BMP2 |
| 5 | GO:0060290 | transdifferentiation | PDX1, SMAD3, CD34 |
| 5 | GO:0060591 | chondroblast differentiation | RARA, FGF4, FGF2, CYR61 |
| 5 | GO:0060718 | chorionic trophoblast cell differentiation | MAP3K4, DNMT3L, E2F7, E2F8 |
| 5 | GO:0003329 | pancreatic PP cell fate commitment | NEUROD1, NKX2-2 |
| 5 | GO:0014034 | neural crest cell fate commitment | SFRP1, WNT8A |
| 5 | GO:0021781 | glial cell fate commitment | NRG1, HES5, SOX2 |
| 5 | GO:0035854 | eosinophil fate commitment | GATA2, GATA1 |
| 5 | GO:0048625 | myoblast fate commitment | PITX1, TCF7L2, EPAS1 |
| 5 | GO:0072560 | type B pancreatic cell maturation | NKX6-1, RFX3 |
| 5 | GO:0051124 | synaptic growth at neuromuscular junction | LRP4, APP |
| 4 | GO:0007529 | establishment of synaptic specificity at neuromuscular junction | CHAT, GPHN, F2R |
| 4 | GO:0060074 | synapse maturation | SHANK1, PALM, PTEN |
| 4 | GO:0008356 | asymmetric cell division | PARD3, ACTR3, ACTR2 |
| 5 | GO:0010070 | zygote asymmetric cell division | RGS14, DICER1 |
| 4 | GO:0021869 | forebrain ventricular zone progenitor cell division | POU3F3, POU3F2, DIXDC1 |
| 5 | GO:0032418 | lysosome localization | HDAC6, LAMTOR1, VPS33B, VPS33A |
| 5 | GO:0051646 | mitochondrion localization | MFN2, MUL1 |
| 5 | GO:0051647 | nucleus localization | DMD, CAV3 |
| 5 | GO:0051648 | vesicle localization | TPGS1, MYO1A |
| 4 | GO:0051668 | localization within membrane | CDH13, RAC1, CNIH2 |
| 5 | GO:0008298 | intracellular mRNA localization | CASC3, STAU1, BICD1 |
| 5 | GO:0006880 | intracellular sequestering of iron ion | FTH1, SRI |
| 5 | GO:0023041 | neuronal signal transduction | NLGN1, P2RY11, NRXN1 |
| 5 | GO:0097527 | necroptotic signaling pathway | RIPK1, TNF, TLR3, FASLG |
| 5 | GO:0070417 | cellular response to cold | FOXO1, NFKBIA |
| 5 | GO:0071470 | cellular response to osmotic stress | PKD2, TRPV4, DDX3X, SLC2A4 |
| 4 | GO:0043503 | skeletal muscle fiber adaptation | MYOD1, ACTA1 |
| 5 | GO:0071453 | cellular response to oxygen levels | MYOD1, LPAR1, UCK2 |
| 5 | GO:0071467 | cellular response to pH | KCNK18, GPLD1, HYAL1 |
| 5 | GO:0071219 | cellular response to molecule of bacterial origin | IRG1, FZD5 |
| 5 | GO:0071226 | cellular response to molecule of fungal origin | CLEC7A, SYK |
| 3 | GO:0060242 | contact inhibition | PTPRJ, TSPO, YAP1 |
| 3 | GO:0060352 | cell adhesion molecule production | GCNT1, GOLPH3 |
| 3 | GO:0072553 | terminal button organization | NLGN2, NLGN1, SNAPIN |
| 3 | GO:0097061 | dendritic spine organization | PICK1, ARF1 |
| 5 | GO:0019043 | establishment of viral latency | CREB3, IRF7 |
| 5 | GO:0019046 | release from viral latency | CREB3, HCFC1 |
| 5 | GO:0019076 | viral release from host cell | PPID, PPIA, IST1 |
| 5 | GO:0046755 | viral budding | TSG101, LRSAM1 |
| 4 | GO:0043163 | cell envelope organization | TGM1, TGM3 |
| 5 | GO:0002176 | male germ cell proliferation | DMRT1, EIF2S2, SPINK2 |
| 1 | GO:0022414 | reproductive process | ANTXR1, ANTXR2 |
| 4 | GO:0001547 | antral ovarian follicle growth | GPR149, FOXO3, ESR1 |
| 4 | GO:0046661 | male sex differentiation | DMRT1, FKBP4 |
| 3 | GO:0022601 | menstrual cycle phase | SFRP1, SFRP4, TGFB2, TGFB3 |
| 3 | GO:0043084 | penile erection | EDNRA, AVP, ACVR2A, AVPR1A |
| 3 | GO:0007320 | insemination | P2RX1, TAC1, SEMG1, DDO |
| 4 | GO:0007620 | copulation | ABAT, PI3 |
| 4 | GO:0051856 | adhesion to symbiont | ICAM1, SCARB1, PVRL2 |
| 1 | GO:0023052 | signaling | CCR5, CCL3 |
| 4 | GO:0043932 | ossification involved in bone remodeling | TGFB1, TGFB3, CTHRC1 |
| 4 | GO:0010573 | vascular endothelial growth factor production | GPR56, HIF1A |
| 4 | GO:0032602 | chemokine production | S100A9, S100A8 |
| 5 | GO:0071954 | chemokine (C-C motif) ligand 11 production | CXCR3, TNFSF4 |
| 5 | GO:0032608 | interferon-beta production | TMEM173, TRIM56, IRF7 |
| 5 | GO:0032611 | interleukin-1 beta production | IL1B, MR1, PYCARD, CASP1 |
| 4 | GO:0032623 | interleukin-2 production | SLC11A1, STOML2 |
| 4 | GO:0032633 | interleukin-4 production | TXK, ITK |
| 3 | GO:0002532 | production of molecular mediator involved in inflammatory response | IL4R, CHIA |
| 4 | GO:0002537 | nitric oxide production involved in inflammatory response | SLC7A2, TLR4 |
| 5 | GO:0002540 | leukotriene production involved in inflammatory response | ALOX5AP, ALOX5 |
| 4 | GO:0003012 | muscle system process | TRIM72, SCO2 |
| 5 | GO:0060073 | micturition | KCNMA1, ADRA1A |
| 5 | GO:0070293 | renal absorption | SLC9A3R1, HBB, AKR1C3 |
| 5 | GO:0001976 | neurological system process involved in regulation of systemic arterial blood pressure | DRD2, MECP2, CALCA |
| 5 | GO:0010159 | specification of organ position | HOXA3, BMP4, FOXH1, TBX3 |
| 5 | GO:0021532 | neural tube patterning | PTCH1, RPGRIP1L, TMEM107 |
| 5 | GO:0021796 | cerebral cortex regionalization | EMX2, EMX1, PAX6 |
| 5 | GO:0021871 | forebrain regionalization | WNT7B, LHX1, PGAP1, WNT2B |
| 5 | GO:0021978 | telencephalon regionalization | LHX2, BMP4, BMP2, SHH |
| 4 | GO:0009798 | axis specification | WNT6, APC |
| 5 | GO:0009855 | determination of bilateral symmetry | ALDH1A2, RALDH2 |
| 4 | GO:0065001 | specification of axis polarity | AHI1, BCOR |
| 5 | GO:0010085 | polarity specification of proximal/distal axis | NODAL, WNT8A |
| 4 | GO:0044241 | lipid digestion | PNLIP, CEL, CLPS, PNLIPRP2 |
| 5 | GO:0042637 | catagen | TGFB2, BARX2 |
| 5 | GO:0048820 | hair follicle maturation | ERCC2, RBPJ |
| 4 | GO:0032902 | nerve growth factor production | PCSK6, FURIN |
| 4 | GO:0042596 | fear response | ADRA2A, DRD4, DBH, ADRB1 |
| 3 | GO:0034381 | plasma lipoprotein particle clearance | MSR1, CD36 |
| 4 | GO:0034447 | very-low-density lipoprotein particle clearance | APOC1, APOE, VLDLR |
| 4 | GO:0060437 | lung growth | RSPO2, SPRY2 |
| 4 | GO:0042633 | hair cycle | PTCH2, PPP1R13L, MPZL3, SNRPE |
| 4 | GO:0002248 | connective tissue replacement involved in inflammatory response wound healing | TGFB1, HIF1A, F2R |
| 4 | GO:0003294 | atrial ventricular junction remodeling | GJA1, GJA5 |
| 4 | GO:0048871 | multicellular organismal homeostasis | PPP1R13L, TENC1, NDN |
| 3 | GO:0050878 | regulation of body fluid levels | PDSS2, HEG1, EPHB2 |
| 5 | GO:0050882 | voluntary musculoskeletal movement | HIPK2, ITPR1 |
| 5 | GO:0050883 | musculoskeletal movement, spinal reflex action | DRD3, CACNA1A |
| 4 | GO:0007509 | mesoderm migration involved in gastrulation | EPB41L5, T |
| 5 | GO:0042249 | establishment of planar polarity of embryonic epithelium | FOXF2, CELSR1 |
| 4 | GO:0060197 | cloacal septation | TP63, BMP4, WNT11 |
| 3 | GO:0035922 | foramen ovale closure | TBX20, GJA5 |
| 2 | GO:0009838 | abscission | SPG20, IST1 |
| 5 | GO:0061042 | vascular wound healing | MCAM, CD34, HPSE |
| 4 | GO:0001705 | ectoderm formation | LHX1, FOXA2 |
| 5 | GO:0048320 | axial mesoderm formation | EPHA2, AXIN1 |
| 5 | GO:0048341 | paraxial mesoderm formation | HTT, LEF1, HNF1A, FOXC1 |
| 3 | GO:0003188 | heart valve formation | SOX9, SCXA |
| 4 | GO:0003190 | atrioventricular valve formation | SMAD4, HEY1 |
| 4 | GO:0003192 | mitral valve formation | NOTCH1, ZFPM1 |
| 4 | GO:0003193 | pulmonary valve formation | TBX20, GJA5 |
| 4 | GO:0003195 | tricuspid valve formation | ZFPM1, HEY2 |
| 3 | GO:0003207 | cardiac chamber formation | NOTCH1, TBX20 |
| 5 | GO:0003218 | cardiac left ventricle formation | HAND1, TBX5 |
| 5 | GO:0003219 | cardiac right ventricle formation | NOTCH1, HAND1, HAND2, SMARCD3 |
| 3 | GO:0003272 | endocardial cushion formation | TBX20, BMPR1A |
| 4 | GO:0010260 | organ senescence | PDX1, CTGF |
| 5 | GO:0032289 | central nervous system myelin formation | ERCC2, TENM4 |
| 5 | GO:0032290 | peripheral nervous system myelin formation | DICER1, NCMAP |
| 3 | GO:0014028 | notochord formation | EPHA2, T, EFNA1 |
| 3 | GO:0021508 | floor plate formation | SMO, FOXH1, GLI2 |
| 4 | GO:0021623 | oculomotor nerve formation | PHOX2A, TFAP2A |
| 5 | GO:0021722 | superior olivary nucleus maturation | CDK5R1, CDK5R2 |
| 5 | GO:0070977 | bone maturation | GH1, FGFR3 |
| 5 | GO:0034505 | tooth mineralization | COL1A1, AMELX |
| 5 | GO:0001838 | embryonic epithelial tube formation | WNT4, SHANK3, RET |
| 3 | GO:0035802 | adrenal cortex formation | CITED2, WT1 |
| 4 | GO:0048069 | eye pigmentation | LEF1, HPS1 |
| 4 | GO:0021589 | cerebellum structural organization | DAB1, HSPA5 |
| 5 | GO:0021612 | facial nerve structural organization | HOXA1, EGR2, HOXB2, HOXB1 |
| 5 | GO:0021633 | optic nerve structural organization | KCNA2, PAX2 |
| 4 | GO:0001832 | blastocyst growth | ZNF830, UBTF, NBN, SMARCA4 |
| 4 | GO:0048630 | skeletal muscle tissue growth | CHRNA1, IGFBP5, CHRND |
| 5 | GO:0072092 | ureteric bud invasion | SALL1, KIF26B |
| 4 | GO:0060440 | trachea formation | BMP4, TGFBR2, CTNNB1 |
| 4 | GO:0060914 | heart formation | SOX17, BMPR1A |
| 3 | GO:0048859 | formation of anatomical boundary | NODAL, SMAD4, SHH, GDF3 |
| 3 | GO:0060033 | anatomical structure regression | WNT7B, CD248, LEF1, SPI1 |
| 4 | GO:0060032 | notochord regression | GLI2, GLI1 |
| 3 | GO:0060061 | Spemann organizer formation | WNT1, FZD5 |
| 3 | GO:0060214 | endocardium formation | OVOL2, SOX18, SOX17, PROX1 |
| 3 | GO:0060661 | submandibular salivary gland formation | FGF10, CDC42 |
| 5 | GO:0046619 | optic placode formation involved in camera-type eye formation | FRS2, PROX1 |
| 4 | GO:0030910 | olfactory placode formation | AXIN1, SOX2, POU2F1, PROX1 |
| 4 | GO:0060596 | mammary placode formation | LRP6, TBX2, NRG3, TBX3 |
| 3 | GO:0060900 | embryonic camera-type eye formation | STRA6, TWIST1 |
| 3 | GO:0072033 | renal vesicle formation | WNT4, CTNNB1 |
| 3 | GO:0072104 | glomerular capillary formation | NOTCH3, BMP4 |
| 4 | GO:0072277 | metanephric glomerular capillary formation | TCF21, PDGFRB, PDGFRA |
| 3 | GO:0072179 | nephric duct formation | PAX2, GATA3 |
| 4 | GO:0044117 | growth of symbiont in host | PGLYRP3, PGLYRP2, PGLYRP1, PGLYRP4 |
| 2 | GO:0033058 | directional locomotion | GRIN2C, GRIN2A, ARPIN |
| 3 | GO:0003419 | growth plate cartilage chondrocyte proliferation | CER1, NPPC |
| 3 | GO:0014009 | glial cell proliferation | LGI4, SOX11, SOX4, PTK2B |
| 4 | GO:0014010 | Schwann cell proliferation | CTNNB1, NF2 |
| 4 | GO:0048659 | smooth muscle cell proliferation | EDNRA, AGT, NAA35 |
| 3 | GO:0033687 | osteoblast proliferation | LRRC17, OSR2, JUNB, FIGNL1 |
| 3 | GO:0035726 | common myeloid progenitor cell proliferation | UNCX, GSTP1, FLT3 |
| 3 | GO:0048144 | fibroblast proliferation | WNT7B, EDNRA, SP2, AGT |
| 5 | GO:0060750 | epithelial cell proliferation involved in mammary gland duct elongation | TFAP2C, WNT5A, MED1, ESR1 |
| 3 | GO:0051450 | myoblast proliferation | IGF1, MET, HGF, GPX1 |
| 4 | GO:0033278 | cell proliferation in midbrain | FZD3, FZD6 |
| 4 | GO:0002158 | osteoclast proliferation | NPR3, CSF1, TNFSF11 |
| 4 | GO:0032943 | mononuclear cell proliferation | ACE, TGFB1 |
| 4 | GO:0010463 | mesenchymal cell proliferation | HAND2, FGF7, FGF4 |
| 2 | GO:0016265 | death | SLC18A2, TCF15, NR4A2 |
| 3 | GO:0001543 | ovarian follicle rupture | NRIP1, AGT |
| 3 | GO:0001546 | preantral ovarian follicle growth | GPR149, AMH |
| 3 | GO:0001550 | ovarian cumulus expansion | EREG, BMPR1B |
| 3 | GO:0001554 | luteolysis | MMP19, CASP2 |
| 3 | GO:0060112 | generation of ovulation cycle rhythm | KISS1, NPY5R |
| 5 | GO:0045475 | locomotor rhythm | KCNMA1, NPAS2, NAGLU, PTEN |
| 5 | GO:0015993 | molecular hydrogen transport | SLC23A2, ADHFE1 |
| 5 | GO:0043490 | malate-aspartate shuttle | SLC25A13, SLC25A12 |
| 5 | GO:0015918 | sterol transport | ABCG5, ABCG8, NPC1L1 |
| 5 | GO:0015920 | lipopolysaccharide transport | LBP, SCARB1 |
| 4 | GO:0015697 | quaternary ammonium group transport | SLC22A5, SLC22A3, SLC22A4 |
| 4 | GO:0015837 | amine transport | AQP9, SLC22A16, RHCG |
| 4 | GO:0015851 | nucleobase transport | SLC23A2, SLC23A1 |
| 5 | GO:0048227 | plasma membrane to endosome transport | SORT1, RAB11A |
| 5 | GO:1990126 | retrograde transport, endosome to plasma membrane | MICALL1, RAB11B, SNX27 |
| 4 | GO:0030185 | nitric oxide transport | AQP1, EDN1, HBB |
| 5 | GO:0032066 | nucleolus to nucleoplasm transport | NOC2L, WRN, TBRG1 |
| 4 | GO:0035526 | retrograde transport, plasma membrane to Golgi | USP6NL, RAB43 |
| 5 | GO:0042045 | epithelial fluid transport | EDN1, EDNRB, SLC26A6, CSF2 |
| 5 | GO:0046717 | acid secretion | DRD2, DRD3, SLC22A16 |
| 5 | GO:0046967 | cytosol to ER transport | TAP1, TAP2 |
| 5 | GO:0015889 | cobalamin transport | GIF, TCN1, TCN2, CUBN |
| 4 | GO:0070633 | transepithelial transport | CXADR, SLC26A6, GPLD1 |
| 4 | GO:0071985 | multivesicular body sorting pathway | RAB27A, RAB27B, SYTL4, EXPH5 |
| 5 | GO:0034436 | glycoprotein transport | ABCG1, VLDLR |
| 5 | GO:0001941 | postsynaptic membrane organization | CHRNB1, GDNF |
| 5 | GO:0010256 | endomembrane system organization | ARFGEF1, ARFGEF2 |
| 5 | GO:0031579 | membrane raft organization | PPT1, CAV3, DLG1 |
| 5 | GO:0033292 | T-tubule organization | CAV3, ANK2 |
| 5 | GO:0045161 | neuronal ion channel clustering | MTCH1, PICK1 |
| 5 | GO:0048499 | synaptic vesicle membrane organization | AP3D1, SYP |
| 5 | GO:0071709 | membrane assembly | SPTBN1, ANK3 |
| 5 | GO:0071763 | nuclear membrane organization | TOR1A, TOR1B, TOR1AIP1 |
| 5 | GO:0097035 | regulation of membrane lipid distribution | TRIAP1, PRELID1 |
| 5 | GO:0042745 | circadian sleep/wake cycle | TH, NPAS2 |
| 4 | GO:0002357 | defense response to tumor cell | PRF1, PLK5 |
| 5 | GO:0002215 | defense response to nematode | EPX, TNFSF4 |
| 5 | GO:0010193 | response to ozone | SCGB1A1, CYP2E1, NGF, TACR1 |
| 5 | GO:0071731 | response to nitric oxide | CCL19, EGLN1, CCR7 |
| 4 | GO:0001306 | age-dependent response to oxidative stress | SOD2, CLN8, COQ7 |
| 5 | GO:0006982 | response to lipid hydroperoxide | APOA4, GPX3 |
| 3 | GO:0006991 | response to sterol depletion | LYN, INSIG1 |
| 5 | GO:0009414 | response to water deprivation | TH, CD9 |
| 5 | GO:0002246 | wound healing involved in inflammatory response | HMOX1, CD44 |
| 5 | GO:0034059 | response to anoxia | OXTR, CTGF |
| 3 | GO:0035902 | response to immobilization stress | CRHR1, TPH1, CRH, UCN3 |
| 5 | GO:0051788 | response to misfolded protein | F12, HDAC6, CLU |
| 3 | GO:0051409 | response to nitrosative stress | ADH5, GCLM, GCLC, DUSP6 |
| 5 | GO:0051599 | response to hydrostatic pressure | KRT8, NTRK1 |
| 5 | GO:0002023 | reduction of food intake in response to dietary excess | NMUR2, PRLH |
| 5 | GO:0009583 | detection of light stimulus | PDE6B, OPN3 |
| 4 | GO:0009590 | detection of gravity | OTOP1, NOX3 |
| 4 | GO:0016048 | detection of temperature stimulus | NGFR, DRGX |
| 5 | GO:0035995 | detection of muscle stretch | TCAP, CSRP3, TTN |
| 5 | GO:0050974 | detection of mechanical stimulus involved in sensory perception | SERPINE2, ASIC2 |
| 4 | GO:0010996 | response to auditory stimulus | NTRK2, CXCL10, TACR1 |
| 4 | GO:0035994 | response to muscle stretch | TCAP, ANKRD1 |
| 3 | GO:0009991 | response to extracellular stimulus | RASGRP4, RPS19, ACTA1 |
| 4 | GO:0060005 | vestibular reflex | NR4A3, TMC1, TMC2 |
| 4 | GO:0097195 | pilomotor reflex | HPN, ADRA1A, NPNT |
| 4 | GO:0002238 | response to molecule of fungal origin | MYD88, TLR2 |
| 3 | GO:0009595 | detection of biotic stimulus | NLRP3, NOD1, NOD2 |
| 4 | GO:0001562 | response to protozoan | VTCN1, SPN, IER3 |
| 5 | GO:0009609 | response to symbiotic bacterium | GPX1, GPX2 |
| 5 | GO:0009597 | detection of virus | IFIH1, DDX58, TLR3 |
| 5 | GO:0001878 | response to yeast | NCF1, MPO, ELANE, PTX3 |
| 4 | GO:0009624 | response to nematode | IL25, CYP1A1, ITLN1 |
| 4 | GO:0071502 | cellular response to temperature stimulus | HTR1B, HTR2B |
| 4 | GO:0010447 | response to acidity | GPR65, SLC9A1 |
| 5 | GO:0009642 | response to light intensity | SLC24A1, GNAT1, GNAT2 |
| 5 | GO:0009648 | photoperiodism | NMU, CLOCK |
| 3 | GO:0009582 | detection of abiotic stimulus | NPFFR2, TAC1, TIMELESS, TACR1 |
| 4 | GO:0014878 | response to electrical stimulus involved in regulation of muscle adaptation | RPS6KB1, TRIM63, MYOG |
| 4 | GO:0003032 | detection of oxygen | SOD2, CYB5R4, SLC11A2 |
| 5 | GO:0044321 | response to leptin | NR1D1, STAR |
| 5 | GO:0097066 | response to thyroid hormone | HPN, AK2 |
| 4 | GO:0003127 | detection of nodal flow | PKD2, PKD1L1 |
| 5 | GO:0034776 | response to histamine | DRD4, DRD2, DRD3 |
| 5 | GO:0046898 | response to cycloheximide | BCL2L1, GHR |
| 5 | GO:0097338 | response to clozapine | PRKAR2B, PRKACB |
| 5 | GO:0055098 | response to low-density lipoprotein particle | ABCA1, SREBF2, PPARG |
| 5 | GO:0055099 | response to high density lipoprotein particle | ADAM17, ABCG1 |
| 4 | GO:0014873 | response to muscle activity involved in regulation of muscle adaptation | AGT, MYOG |
| 2 | GO:0014854 | response to inactivity | DRD2, IL10 |
| 3 | GO:0009593 | detection of chemical stimulus | DRGX, UGT2A1 |
| 5 | GO:0050968 | detection of chemical stimulus involved in sensory perception of pain | ASIC3, TRPA1 |
| 5 | GO:0046684 | response to pyrethroid | SCN1B, TH, SCN2B, DDC |
| 4 | GO:0060992 | response to fungicide | GRIN1, CYP17A1, STAR, CYP11A1 |
| 5 | GO:0043331 | response to dsRNA | PMAIP1, PELI1 |
| 5 | GO:0070669 | response to interleukin-2 | CITED1, STAT5B, JAK3 |
| 5 | GO:0070671 | response to interleukin-12 | RIPK2, JAK2 |
| 5 | GO:0070672 | response to interleukin-15 | STAT5B, JAK3, ACSL4 |
| 5 | GO:0070741 | response to interleukin-6 | CITED1, CHI3L1, SFTPC, FOXA2 |
| 5 | GO:0071104 | response to interleukin-9 | CITED1, JAK3 |
| 4 | GO:0034465 | response to carbon monoxide | EGR1, KCNMA1, IL10 |
| 4 | GO:0046683 | response to organophosphorus | TYMS, RFC3, AKR1C1, TRIM16 |
| 5 | GO:0010044 | response to aluminum ion | MAOB, QDPR, LONP1 |
| 5 | GO:0032025 | response to cobalt ion | D2HGDH, CASP8 |
| 4 | GO:0010157 | response to chlorate | PTCH1, PDX1 |
| 4 | GO:0034021 | response to silicon dioxide | SOD2, SCGB1A1 |
| 3 | GO:0050906 | detection of stimulus involved in sensory perception | PPEF2, PPEF1 |
| 4 | GO:0008105 | asymmetric protein localization | SCRIB, WNT7A, COLQ, DYNC2H1 |
| 5 | GO:0045175 | basal protein localization | NCKAP1, ERBB2IP |
| 4 | GO:0031503 | protein complex localization | KIF17, BIRC5, DNMT3B, FKBP4 |
| 5 | GO:0071896 | protein localization to adherens junction | SCRIB, DSP, MPP7 |
| 3 | GO:1901998 | toxin transport | SLC17A3, LRP6, ABCG1, SLC7A8 |
| 5 | GO:0071169 | establishment of protein localization to chromatin | CCDC101, LRWD1 |
| 3 | GO:0051303 | establishment of chromosome localization | NDE1, BIRC5 |
| 4 | GO:0051310 | metaphase plate congression | CENPF, SPICE1 |
| 5 | GO:0032401 | establishment of melanosome localization | RAB17, SHROOM2 |
| 5 | GO:0051877 | pigment granule aggregation in cell center | MKKS, BBS4, BBS7 |
| 3 | GO:0051654 | establishment of mitochondrion localization | PVRL2, FEZ1 |
| 3 | GO:0051683 | establishment of Golgi localization | ARHGAP21, COPG1, CDC42 |
| 2 | GO:0009405 | pathogenesis | TMEM181, MECP2, CARM1 |
| 3 | GO:0051702 | interaction with symbiont | GPX1, GPX2 |
| 5 | GO:0002920 | regulation of humoral immune response | CD37, SPNS2, CXCL13 |
| 3 | GO:0006808 | regulation of nitrogen utilization | BCL2, BAX |
| 5 | GO:0009890 | negative regulation of biosynthetic process | GCHFR, GSTP1 |
| 5 | GO:0060267 | positive regulation of respiratory burst | INSR, CAMK1D, INS |
| 4 | GO:0032350 | regulation of hormone metabolic process | FSHR, TCF7L2 |
| 4 | GO:0060263 | regulation of respiratory burst | RAC2, RAC1, NOXO1, NOXA1 |
| 5 | GO:0051712 | positive regulation of killing of cells of other organism | NOS2, IFNG, FCER2 |
| 5 | GO:0031652 | positive regulation of heat generation | SLC27A1, APLN |
| 5 | GO:2000189 | positive regulation of cholesterol homeostasis | NR1D1, ACOX1, NR1H3, HNF4A |
| 5 | GO:2000507 | positive regulation of energy homeostasis | SGIP1, PPARGC1A |
| 5 | GO:0003254 | regulation of membrane depolarization | FHL1, NEDD4L, RANGRF |
| 5 | GO:0061088 | regulation of sequestering of zinc ion | SLC30A8, SLC30A4, SLC30A3, AP3D1 |
| 4 | GO:2000188 | regulation of cholesterol homeostasis | NR1D1, SREBF2, FGFR4 |
| 5 | GO:0060178 | regulation of exocyst localization | RALB, RALGAPA2, RALGAPB |
| 5 | GO:0060632 | regulation of microtubule-based movement | IGBP1, MAPT, HDAC6 |
| 5 | GO:0001560 | regulation of cell growth by extracellular stimulus | KIF26A, PPP1R9B, MYOCD |
| 4 | GO:0040009 | regulation of growth rate | PARP1, WRN, BNIPL |
| 5 | GO:0060420 | regulation of heart growth | DUSP6, MYH6 |
| 4 | GO:0042753 | positive regulation of circadian rhythm | BTRC, FBXW11 |
| 5 | GO:0060406 | positive regulation of penile erection | EDNRB, OXT, OXTR, P2RY1 |
| 5 | GO:0033623 | regulation of integrin activation | FBLIM1, FARP2, SELP |
| 5 | GO:0060491 | regulation of cell projection assembly | CCL19, FAM110C |
| 4 | GO:0090083 | regulation of inclusion body assembly | SNCAIP, BAG5 |
| 5 | GO:0090084 | negative regulation of inclusion body assembly | SACS, HSPA1A, DNAJB2 |
| 5 | GO:1900106 | positive regulation of hyaluranon cable assembly | HAS3, BMP7, HYAL1 |
| 4 | GO:1901888 | regulation of cell junction assembly | RAPGEF1, RAPGEF2, RAP1B, RAP1A |
| 5 | GO:0043243 | positive regulation of protein complex disassembly | TNF, MGEA5, BNIP3 |
| 5 | GO:0050867 | positive regulation of cell activation | JAK2, CTGF |
| 5 | GO:0090343 | positive regulation of cell aging | LMNA, TP53 |
| 5 | GO:0060760 | positive regulation of response to cytokine stimulus | TAF9, WNT5A |
| 5 | GO:0010902 | positive regulation of very-low-density lipoprotein particle remodeling | APOC2, APOA5 |
| 5 | GO:0060279 | positive regulation of ovulation | PLAT, INHBA, INHBB |
| 5 | GO:0010716 | negative regulation of extracellular matrix disassembly | CST3, FAP, DPP4 |
| 5 | GO:0043242 | negative regulation of protein complex disassembly | SLN, TNF, HDAC6, IRAK3 |
| 5 | GO:0051782 | negative regulation of cell division | PTCH1, TXNIP, BLM, MYC |
| 5 | GO:0090288 | negative regulation of cellular response to growth factor stimulus | CASK, SLIT2 |
| 5 | GO:2000360 | negative regulation of binding of sperm to zona pellucida | ASTL, ZP3, ZP4 |
| 5 | GO:0010903 | negative regulation of very-low-density lipoprotein particle remodeling | APOC3, APOA1, APOA2 |
| 5 | GO:0050819 | negative regulation of coagulation | PROCR, HS3ST5, ANXA5, ANXA4 |
| 5 | GO:1900222 | negative regulation of beta-amyloid clearance | LRPAP1, SRF, MYOCD |
| 5 | GO:0047484 | regulation of response to osmotic stress | MLC1, TRPV4, GYPA |
| 5 | GO:0061041 | regulation of wound healing | PLAU, VIL1 |
| 4 | GO:2001023 | regulation of response to drug | ADIRF, GABRA4 |
| 5 | GO:2001038 | regulation of cellular response to drug | NCOA1, HMGA2 |
| 5 | GO:0010453 | regulation of cell fate commitment | FGFR2, PAX7 |
| 5 | GO:0051147 | regulation of muscle cell differentiation | SUPT6H, CAMK1, MEGF10 |
| 5 | GO:0010649 | regulation of cell communication by electrical coupling | CASQ2, TRDN, ASPH, SRI |
| 5 | GO:1901214 | regulation of neuron death | RILPL1, SARM1, DHCR24 |
| 4 | GO:0032878 | regulation of establishment or maintenance of cell polarity | IGF1, LLGL2, TEK |
| 4 | GO:0032970 | regulation of actin filament-based process | PARD3, CNN2, FRMD6 |
| 5 | GO:0090170 | regulation of Golgi inheritance | MAPK3, MAPK1, MAP2K2, MAP2K1 |
| 5 | GO:1900063 | regulation of peroxisome organization | MAVS, DNM1L, MFF |
| 5 | GO:0014842 | regulation of satellite cell proliferation | PAXBP1, CFLAR, ANGPT1, MYOG |
| 5 | GO:0033688 | regulation of osteoblast proliferation | RHOA, NPR3, FGFR2 |
| 5 | GO:0072091 | regulation of stem cell proliferation | AGO3, SOX18, SOX17, YAP1 |
| 5 | GO:2000254 | regulation of male germ cell proliferation | RHBDD1, RSPO1 |
| 5 | GO:0051823 | regulation of synapse structural plasticity | CAMK2B, CTNNA2, NCAN, DMPK |
| 5 | GO:0009786 | regulation of asymmetric cell division | POU5F1, WNT9B |
| 5 | GO:2000035 | regulation of stem cell division | SFRP2, SOX17 |
| 4 | GO:0060968 | regulation of gene silencing | HIST1H3A, CDK2 |
| 5 | GO:2000327 | positive regulation of ligand-dependent nuclear receptor transcription coactivator activity | RQCD1, CNOT6 |
| 5 | GO:0032649 | regulation of interferon-gamma production | RIPK3, ISG15, CCR7 |
| 5 | GO:0032675 | regulation of interleukin-6 production | MAPKAPK2, HLA-B, AFAP1L2 |
| 5 | GO:0032680 | regulation of tumor necrosis factor production | MAPKAPK2, TBC1D23, ZFP36, LTF |
| 5 | GO:0034344 | regulation of type III interferon production | IFIH1, DDX58 |
| 5 | GO:0010988 | regulation of low-density lipoprotein particle clearance | HNRNPK, CNPY2, FGF21 |
| 4 | GO:0034103 | regulation of tissue remodeling | CST3, TP53, THBS4 |
| 5 | GO:0046850 | regulation of bone remodeling | INPP4B, SUCO, GJA1 |
| 4 | GO:0042634 | regulation of hair cycle | NIPBL, FA2H |
| 5 | GO:0044065 | regulation of respiratory system process | MTG2, MTG1, FTO |
| 3 | GO:0051917 | regulation of fibrinolysis | APOH, FAP |
| 3 | GO:0097006 | regulation of plasma lipoprotein particle levels | LPCAT3, DGAT2 |
| 3 | GO:1900271 | regulation of long-term synaptic potentiation | NLGN3, SHANK3 |
| 4 | GO:0080154 | regulation of fertilization | RNASE10, ASUN, PLCB1 |
| 3 | GO:0001505 | regulation of neurotransmitter levels | ZNF219, GABRA2, PDE1B, DVL1 |
| 4 | GO:0014916 | regulation of lung blood pressure | GCH1, BMPR2 |
| 5 | GO:0003085 | negative regulation of systemic arterial blood pressure | NEDD4L, IER3, BBS4, BMPR2 |
| 3 | GO:0010817 | regulation of hormone levels | BCAT2, FOXA3, FOXA2, SOX8 |
| 5 | GO:0045759 | negative regulation of action potential | CNR1, CNR2, CHRNB2 |
| 5 | GO:0086001 | regulation of cardiac muscle cell action potential | DMD, PKP2 |
| 5 | GO:0010917 | negative regulation of mitochondrial membrane potential | PMAIP1, PRELID1 |
| 4 | GO:0045838 | positive regulation of membrane potential | PIAS3, ANK3, GIMAP5 |
| 5 | GO:0010918 | positive regulation of mitochondrial membrane potential | STOML2, BAD |
| 5 | GO:0086010 | membrane depolarization involved in regulation of action potential | YWHAH, SCN3B, KCNH2, SCN5A |
| 4 | GO:0060075 | regulation of resting membrane potential | KCNJ10, PSEN1, KCNJ2 |
| 4 | GO:0086036 | regulation of cardiac muscle cell membrane potential | ATP2A2, TRDN, EHD3, PLN |
| 5 | GO:0030104 | water homeostasis | IGF1, AQP9, NEDD4L, GHRHR |
| 5 | GO:0050801 | ion homeostasis | WNK4, KLHL3, AMELX, CRH |
| 3 | GO:0050803 | regulation of synapse structure and activity | PPT1, APP, SYNGAP1 |
| 5 | GO:0030730 | sequestering of triglyceride | IL1B, TNF, ENPP1 |
| 5 | GO:0032119 | sequestering of zinc ion | S100A9, S100A8, SLC30A8, SLC30A7 |
| 5 | GO:0051208 | sequestering of calcium ion | ATP7B, CALR, CASQ2, HSP90B1 |
| 5 | GO:0035565 | regulation of pronephros size | HNF1B, HNF1A |
| 5 | GO:0035566 | regulation of metanephros size | PAX2, AGTR2 |
| 3 | GO:0040030 | regulation of molecular function, epigenetic | ASIP, CTCF |
| 4 | GO:0051100 | negative regulation of binding | CYP2D6, YBX2, P2RY1 |
| 5 | GO:0035562 | negative regulation of chromatin binding | TDG, WAPAL, MEPCE, SENP2 |
| 5 | GO:1901877 | negative regulation of calcium ion binding | SLN, PLN |
| 5 | GO:0001845 | phagolysosome assembly | P2RX7, SRPX, CORO1A, MYO7A |
| 4 | GO:0010324 | membrane invagination | FCHO2, FNBP1L |
| 4 | GO:0016557 | peroxisome membrane biogenesis | PEX11A, PEX19, PEX16, PEX3 |
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