Difference between revisions of "BIO project GO-term table"

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Roughly, this selection works as follows:
 
Roughly, this selection works as follows:
−
1 Retrieve the ontology terms, and the list of annotated human genes from the database.
+
 
−
# Remove all terms that are not in the ''biological process'' ontology.
+
1. Retrieve the ontology terms, and the list of annotated human genes from the database.
−
# Associate all genes with their respective terms
+
2. Remove all terms that are not in the ''biological process'' ontology.
−
# Remove all terms that are leafs (no children) AND have no genes annotated. (Doing this once generates more such leafs; iterate until all such nodes have been removed.
+
3. Associate all genes with their respective terms
−
# For each term, find all descendants.
+
4. Remove all terms that are leafs (no children) AND have no genes annotated. (Doing this once generates more such leafs; iterate until all such nodes have been removed.
−
# Of all descendants, collect all annotated genes.
+
5. For each term, find all descendants.
−
# Make the list of genes unique. This is important since there may be more than one path to a gene and we don't want to double count it.
+
6. Of all descendants, collect all annotated genes.
−
# Store the number of genes associated to a term and its descendants.
+
7. Make the list of genes unique. This is important since there may be more than one path to a gene and we don't want to double count it.
−
# Select terms that have 3 to 5 associated genes.
+
8. Store the number of genes associated to a term and its descendants.
−
# Remove terms that contain certain keywords that may make the process less suitable for our purposes, such as "development", "morphogenesis", "behavior".
+
9. Select terms that have 3 to 5 associated genes.
−
# Write the remaining terms into a Wiki table format, with links to GO terms and genes.
+
10. Remove terms that contain certain keywords that may make the process less suitable for our purposes, such as "development", "morphogenesis", "behavior".
 +
11. Write the remaining terms into a Wiki table format, with links to GO terms and genes.
  
 
Details below.
 
Details below.
Line 46: Line 47:
 
  Q14209    E2F2        GO:0051726  GO_REF:0000019  IEA           Transcription factor E2F2  taxon:9606
 
  Q14209    E2F2        GO:0051726  GO_REF:0000019  IEA           Transcription factor E2F2  taxon:9606
  
−
:'''2.''' I downloaded the GO term file <code>go-basic.obo</code> from its repository [http://geneontology.org/page/download-ontology at '''GO''' -the Gene Ontology Consortium]. It contains the actual ontology terms (45,896 terms), they look like this (some information omitted).
+
:'''2.''' I downloaded the GO term file <code>go-basic.obo</code> from its repository [http://geneontology.org/page/download-ontology at '''GO''' - the Gene Ontology Consortium]. It contains the actual ontology terms (45,896 terms), they look like this (some information omitted).
  
−
[Term]
+
[Term]
−
id: GO:0051726
+
id: GO:0051726
−
name: regulation of cell cycle
+
name: regulation of cell cycle
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namespace: biological_process
+
namespace: biological_process
−
def: "Any process that modulates the rate or extent of progression through the cell cycle." [GOC:ai, GOC:dph, GOC:tb]
+
def: "Any process that modulates the rate or extent of progression through the cell cycle." [GOC:ai, GOC:dph, GOC:tb]
−
is_a: GO:0050794 ! regulation of cellular process
+
is_a: GO:0050794 ! regulation of cellular process
−
relationship: regulates GO:0007049 ! cell cycle
+
relationship: regulates GO:0007049 ! cell cycle
  
−
: Note the <code>is_a</code> relationship that points to the '''parent''' node, of which this one is a specialization. This means: the terms have parent-associations listed with them, but don't list child terms. We need to construct the list of child terms for each node to look for associated genes.
+
: Note the <code>is_a</code> relationship that points to the '''parent''' term, <tt>GO:0050794</tt>, of which <tt>GO:0051726</tt> is a specialization. This means: the terms have parent-associations listed with them, but don't list child terms. This means we can go up to the root from each term, but we can't descend. We need to record the child terms for each node, to be able to navigate both up and down through the ontology.
  
−
:'''3.''' I reconstructed the DAG (Directed Acyclic Graph) by connecting each of the  nodes to its parent node.
+
:'''3.''' Open this file in '''R''' and read all the terms that are labelled as <tt>namespace: biological_process</tt> into a data frame storing ID, name, definition, and parent term IDs. These are 29,309 terms. Then add each term ID to its parent terms as a child term.
  
−
:'''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.
+
:'''4.''' Open the human GOA file and read all gene annotations into a data frame. These are 392,942. That's a lot - we expect at least three annotations for each of the 19,225 genes that GOA currently contains, one for each ontology, but we find on average 20 annotations. Next, add each gene symbol to the term data frame, if the annotation's GO ID is in our set.
  
−
:'''5.''' For each node, I counted its distance from the root node. This "depth" tells us a bit about how specific a term is.
+
:'''5.''' Next, remove all terms that are leaves (i.e. they don't have children), AND have no annotated genes. These are terms that might be specific to fungi, prokaryotes, viruses or similar. Since our goal is to count the number of genes associated with each term, those can't contribute since their own count is zero. Deleting those nodes obviously creates new leaves in the ontology, so this process has to be iterated, until no more nodes can be removed. This deletes 11,733 terms from the ontology.
  
−
:'''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.
+
:'''6.''' We need a function that finds all descendants of a term. In order to find and visit all descendants, start from a term and put its child(ren) into a queue. While the queue is not empty, remove the first ID from the queue, and add those of its children to the queue that we haven't visited before.
  
−
:'''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:
+
:'''7.''' For each term, count all genes that are associated to it or to any of its descendants. The root term, <tt>GO:0008150</tt> has 17,030 associated genes.
  
−
01  GO:0002376  immune system process [ ADSS ... 17 genes ]
+
:'''8.''' Next, select all terms that have from three to five associated genes AND contain none of a list of keywords. These keywords include: "proliferation", "development", "morphogenesis", "regression", "induction", "maturation", "formation", "growth", "*bolic process", "biosynthetic process", and "behavior". I feel that even though the GO terms may be manageable, the actual '''system''' would likely contain an unwieldy number of genes. I also removed all "positive regulation of ...", and "negative regulation of ..." terms. These always have a parent term:  "regulation of ..." and that term would be the right one to consider.
−
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: <code>MECOM</code> is involved in the homeostasis (keeping cell-numbers constant) of neutrophil white blood cells. <code>MEN1</code> is 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. <code>ADSS</code> seems 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.
+
:'''9.''' Finally, the 1,224 selected terms were written into a [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/BCH441_2016_project_GO_term_table table in an editable Wiki code format], including links to GO and UniProt.
  
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:'''8.''' Next, I selected from this list. For this project we are looking for terms that give a good approximation of a biological system, 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.
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{{Vspace}}
−
 
 
−
:'''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 [http://www.genenames.org/ '''HGNC'''] so I would expect all of the genes to be findable at UniProt.
 
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&nbsp;
 
  
 
===How to use the table to adopt a function and define a "system" for the project===
 
===How to use the table to adopt a function and define a "system" for the project===

Revision as of 15:37, 26 November 2016

GO term Table


Almost done ... but still in progress right now,


 

Extracting gene functions from GO and GOA

The table of selected biological process GO terms a starting point for system definition and gene selection.


The objective of selecting GO terms from the ontology is to find nodes that have a small number of genes associated to them (or their children). If the number of annotated genes is too small, not enough may be known about the system to usefully model it. If the number is too large, modelling the system will be too time consuming for the scope of a class project. It is also highly likely that the system should actually be broken down into subsystems, which ought to be modelled individually. I have chosen GO terms with from three to five annotated genes as a cutoff that seems workable.

Roughly, this selection works as follows:

1. Retrieve the ontology terms, and the list of annotated human genes from the database. 2. Remove all terms that are not in the biological process ontology. 3. Associate all genes with their respective terms 4. Remove all terms that are leafs (no children) AND have no genes annotated. (Doing this once generates more such leafs; iterate until all such nodes have been removed. 5. For each term, find all descendants. 6. Of all descendants, collect all annotated genes. 7. Make the list of genes unique. This is important since there may be more than one path to a gene and we don't want to double count it. 8. Store the number of genes associated to a term and its descendants. 9. Select terms that have 3 to 5 associated genes. 10. Remove terms that contain certain keywords that may make the process less suitable for our purposes, such as "development", "morphogenesis", "behavior". 11. Write the remaining terms into a Wiki table format, with links to GO terms and genes.

Details below.

 

Creation of the Process Table

The Process Table was created in the following steps:

1. I downloaded the most recent version of goa_human.gaf from the GOA repository at the EBI, released on November 22. 2016. The file contains gene names and GO terms - here is one line of the contents (selected columns):
UniProtID  GeneSymbol  GOtermID    Reference       EvidenceCode  Description                taxID
Q14209     E2F2        GO:0051726  GO_REF:0000019  IEA	          Transcription factor E2F2  taxon:9606
2. I downloaded the GO term file go-basic.obo from its repository at GO - the Gene Ontology Consortium. It contains the actual ontology terms (45,896 terms), they look like this (some information omitted).
[Term]
id: GO:0051726
name: regulation of cell cycle
namespace: biological_process
def: "Any process that modulates the rate or extent of progression through the cell cycle." [GOC:ai, GOC:dph, GOC:tb]
is_a: GO:0050794 ! regulation of cellular process
relationship: regulates GO:0007049 ! cell cycle
Note the is_a relationship that points to the parent term, GO:0050794, of which GO:0051726 is a specialization. This means: the terms have parent-associations listed with them, but don't list child terms. This means we can go up to the root from each term, but we can't descend. We need to record the child terms for each node, to be able to navigate both up and down through the ontology.
3. Open this file in R and read all the terms that are labelled as namespace: biological_process into a data frame storing ID, name, definition, and parent term IDs. These are 29,309 terms. Then add each term ID to its parent terms as a child term.
4. Open the human GOA file and read all gene annotations into a data frame. These are 392,942. That's a lot - we expect at least three annotations for each of the 19,225 genes that GOA currently contains, one for each ontology, but we find on average 20 annotations. Next, add each gene symbol to the term data frame, if the annotation's GO ID is in our set.
5. Next, remove all terms that are leaves (i.e. they don't have children), AND have no annotated genes. These are terms that might be specific to fungi, prokaryotes, viruses or similar. Since our goal is to count the number of genes associated with each term, those can't contribute since their own count is zero. Deleting those nodes obviously creates new leaves in the ontology, so this process has to be iterated, until no more nodes can be removed. This deletes 11,733 terms from the ontology.
6. We need a function that finds all descendants of a term. In order to find and visit all descendants, start from a term and put its child(ren) into a queue. While the queue is not empty, remove the first ID from the queue, and add those of its children to the queue that we haven't visited before.
7. For each term, count all genes that are associated to it or to any of its descendants. The root term, GO:0008150 has 17,030 associated genes.
8. Next, select all terms that have from three to five associated genes AND contain none of a list of keywords. These keywords include: "proliferation", "development", "morphogenesis", "regression", "induction", "maturation", "formation", "growth", "*bolic process", "biosynthetic process", and "behavior". I feel that even though the GO terms may be manageable, the actual system would likely contain an unwieldy number of genes. I also removed all "positive regulation of ...", and "negative regulation of ..." terms. These always have a parent term: "regulation of ..." and that term would be the right one to consider.
9. Finally, the 1,224 selected terms were written into a table in an editable Wiki code format, including links to GO and 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:

Complete GO annotation...

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 function. 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 to my example project).

I suggest you leave the code for the CC license in place. Why? ...

I put code for a Creative Commons Attribution 4.0 International (CC) license on the template for your project pages, anticipating that the material might become useful beyond the course at some point - suitably validated - to contribute to a training set for algorithms that automate systems discovery. The CC license is one of the standards for open-sourcing work in our domain; this variant of the license allows reproduction but requires those who produce derivative work to keep the original author names associated with the material.

This license does not mean I am CC-licensing the template so you can copy my work ... no: the license is there to make it easier for others to continue based on your ideas. The copyright status of course work and whether and how it can feed into further research is complex: on one hand the author is the author. On the other hand, such work is produced at a lecturers direction, feedback and instructions. Moreover there are fair-use and educational exceptions, non-commercial exceptions and the question what part of such a collation could be copyrighted in the first place, much of it being as it were derivative of public databases. In this context, attaching a CC license provides some clarity: any future use and reference should attribute it properly and move on.

If you like the idea that your work could perhaps become useful, and have your name associated with such use, then leave the license code on the page.

Some references:



 

The Function Table

 

Depth GO Term Text Genes
5GO:0001776leukocyte homeostasisMEN1, FLT3, NKX2-3
3GO:0016445somatic diversification of immunoglobulinsAICDA, CTNNBL1, RAG2
5GO:0002366leukocyte activation involved in immune responseSH2D1B, CLEC7A, SYK
5GO:0019724B cell mediated immunitySLA2, MSH2, FAS
4GO:0002679respiratory burst involved in defense responseNCF1, MPO, PIK3CG, PIK3CD
5GO:0045728respiratory burst after phagocytosisHCK, SELK
3GO:0002352B cell negative selectionBAX, BAK1
4GO:0002367cytokine production involved in immune responseMR1, NOD2
3GO:0002377immunoglobulin productionFAS, IL7R
4GO:0002381immunoglobulin production involved in immunoglobulin mediated immune responseHLA-DQB1, HLA-DRB1, NOD2
3GO:0002513tolerance induction to self antigenLYN, FOXP3, TGFB1
4GO:0002384hepatic immune responseIL6, IL6R
4GO:0002418immune response to tumor cellPRF1, MICA
3GO:0042092type 2 immune responseIL4, BCL6, IL18, IL10
4GO:0002495antigen processing and presentation of peptide antigen via MHC class IIMARCH1, MARCH8
2GO:0045058T cell selectionCD1D, CD4, CD74
3GO:0043366beta selectionZAP70, SYK
3GO:0043368positive T cell selectionTHEMIS, BCL11B
3GO:0045061thymic T cell selectionCARD11, JAG2, GATA3
5GO:0050902leukocyte adhesive activationCX3CL1, SELPLG
5GO:0018916nitrobenzene metabolic processGSTM1, GSTM2, GSTM3
5GO:0006579amino-acid betaine catabolic processBHMT, DMGDH
5GO:0033076isoquinoline alkaloid metabolic processCYP2D6, TH, DDC
5GO:0000255allantoin metabolic processSTAT5B, STAT5A, GHR
5GO:0009822alkaloid catabolic processCYP2D6, CYP3A4, CYP3A5
5GO:0070458cellular detoxification of nitrogen compoundGSTM1, GSTM2, GSTM3
4GO:0051410detoxification of nitrogen compoundMARC1, MARC2
4GO:0009820alkaloid metabolic processCYP2D6, CYP1A2
5GO:0042412taurine biosynthetic processCDO1, CSAD
2GO:0009056catabolic processTMEM150A, CES2, PTER
5GO:0042447hormone catabolic processECE1, ACE, IDE
5GO:0044242cellular lipid catabolic processACADL, MT3
4GO:0046185aldehyde catabolic processALDH3B1, GPI, AKR1A1
5GO:0046294formaldehyde catabolic processESD, ADH5
5GO:0046952ketone body catabolic processBDH1, ACAT1, OXCT1, OXCT2
5GO:0006706steroid catabolic processSTS, CYP1A2, HSD17B14, CYP3A4
5GO:0044240multicellular organismal lipid catabolic processPLA2G1B, APOA4
5GO:0016139glycoside catabolic processGBA2, GBA3, NAGA, GLA
5GO:0000272polysaccharide catabolic processCHIT1, CHIA
4GO:0016052carbohydrate catabolic processPGM2, PGM2L1, NAGA, AMY2A
3GO:0010025wax biosynthetic processFAR1, AWAT2
5GO:0070814hydrogen sulfide biosynthetic processMPST, CBS, CTH
5GO:0002378immunoglobulin biosynthetic processGALNT2, PTPRC
4GO:0006082organic acid metabolic processCYP2C8, FMO2, FMO1
4GO:0015980energy derivation by oxidation of organic compoundsACSM1, ACADVL
4GO:0018894dibenzo-p-dioxin metabolic processCYP1A2, CYP17A1, STAR, CYP11A1
4GO:0000103sulfate assimilationSULT2B1, PAPSS1, PAPSS2
4GO:0019417sulfur oxidationMICAL1, MICAL2
5GO:0030388fructose 1,6-bisphosphate metabolic processPFKL, ALDOA, ALDOC, ALDOB
5GO:0017143insecticide metabolic processCYP1A1, STAR
5GO:0052314phytoalexin metabolic processTH, DDC
4GO:0016999antibiotic metabolic processTXN, DPEP1
4GO:0042133neurotransmitter metabolic processGCHFR, CLN3, CACNA1A, AGTPBP1
4GO:0042180cellular ketone metabolic processCYP2B6, DHRS4
5GO:1901661quinone metabolic processCRYZL1, ADH4
5GO:0006643membrane lipid metabolic processAGMO, B4GALT4
5GO:0006720isoprenoid metabolic processPHYH, GGPS1
5GO:0046485ether lipid metabolic processTMEM86B, AGMO, HRASLS
3GO:0072592oxygen metabolic processNOX1, ME3, FMO2
4GO:0042743hydrogen peroxide metabolic processNOX1, PARK7
4GO:0005976polysaccharide metabolic processCHST1, CHST7, TYMS
5GO:0070085glycosylationCLN5, COG6
5GO:0042982amyloid precursor protein metabolic processKLK6, DLG1, LDLRAP1, ACHE
5GO:1990000amyloid fibril formationRIPK1, RIPK3
3GO:0044236multicellular organismal metabolic processGHR, TIPARP, MNAT1
4GO:0044259multicellular organismal macromolecule metabolic processTUB, AKR1C3
5GO:0002268follicular dendritic cell differentiationBCL3, NFKB2
4GO:0014719satellite cell activationWNT7A, MEGF10
4GO:0048143astrocyte activationAGT, ADORA2A
4GO:0072537fibroblast activationRGCC, IL17A, IL17RA
4GO:0016080synaptic vesicle targetingNLGN1, SCRIB, PSEN1, SEPT5
5GO:0048203vesicle targeting, trans-Golgi to endosomeAP1AR, WIPI1
5GO:0030050vesicle transport along actin filamentFNBP1L, WASL
5GO:0031022nuclear migration along microfilamentSYNE2, SUN2
5GO:0070358actin polymerization-dependent cell motilityJMY, NCKAP1L, EPS8
5GO:0097491sympathetic neuron projection guidanceNRP1, NRP2, SEMA3A, SEMA3F
3GO:0006949syncytium formationERCC1, CCNG1, ERVW-1
5GO:0006999nuclear pore organizationNUP98, SEH1L, NUP133, TPR
5GO:0007000nucleolus organizationNOLC1, RRN3, RPS19, PES1
5GO:0007290spermatid nucleus elongationTNP1, H1FNT, KDM3A
5GO:0030382sperm mitochondrion organizationPVRL2, SEPT4
5GO:0090161Golgi ribbon formationOPTN, TMED5, GCC2
5GO:0090166Golgi disassemblyPLK3, VRK1
4GO:0007033vacuole organizationMAN2A1, FIG4, NDP
5GO:0006900membrane buddingP2RX7, FNBP1L, WASL
5GO:0030719P granule organizationPLD6, TDRD5
4GO:0031023microtubule organizing center organizationPAFAH1B1, CLASP2, CLASP1, GCC2
5GO:0000715nucleotide-excision repair, DNA damage recognitionXPC, RAD23B
5GO:0000819sister chromatid segregationTOP2B, TOP2A, LATS1
5GO:0006344maintenance of chromatin silencingHDAC2, UBE2B, SIRT1
5GO:0000022mitotic spindle elongationPRC1, KIF23
5GO:0098535de novo centriole assemblyCCDC78, PLK4, CEP152, CCDC67
3GO:0007028cytoplasm organizationTFCP2L1, RRN3, KIF5B
4GO:0007296vitellogenesisZMIZ1, FOSL1
5GO:0007113endomitotic cell cycleUBA3, CIB1, PLK3
5GO:0007060male meiosis chromosome segregationTEX11, MLH1
5GO:0045143homologous chromosome segregationESPL1, MSH4, MSH5
5GO:0021937cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferationLHX5, LHX1
5GO:0035425autocrine signalingHILPDA, FZD1
5GO:0038001paracrine signalingPDGFB, CD34
5GO:0060638mesenchymal-epithelial cell signalingHOXA5, WNT5A, WNT2B
5GO:0060684epithelial-mesenchymal cell signalingWNT6, SMO, BMP4, CDC42
4GO:0007412axon target recognitionUCHL1, BDNF, FOXB1, STXBP1
4GO:0010643cell communication by chemical couplingDBN1, GJA1
4GO:0010644cell communication by electrical couplingDBN1, GJA1
5GO:0071460cellular response to cell-matrix adhesionSKP2, DSPP
4GO:0035426extracellular matrix-cell signalingFZD4, FER, NDP
5GO:0086067AV node cell to bundle of His cell communicationCXADR, SCN10A, SCN5A, SCN4B
5GO:0086070SA node cell to atrial cardiac muscle cell communicationSCN3B, ANK2, SCN5A
5GO:0006931substrate-dependent cell migration, cell attachment to substrateEPB41L5, TNFRSF12A, CUZD1
5GO:0003365establishment of cell polarity involved in ameboidal cell migrationAMOTL1, AMOT
5GO:0045200establishment of neuroblast polarityDOCK7, FGF13, RAB10
4GO:0030011maintenance of cell polarityDST, NCKAP1L, ATN1
5GO:0001300chronological cell agingENG, SERPINE1
5GO:0001302replicative cell agingERCC1, WRN, ROMO1
5GO:0043654recognition of apoptotic cellJMJD6, PEAR1, SCARB1, MEGF10
5GO:0016198axon choice point recognitionGAP43, EFNB3
5GO:0070593dendrite self-avoidanceDSCAM, DSCAML1
4GO:0009988cell-cell recognitionCLEC4M, FUT3, CD209, ST6GALNAC6
5GO:0001771immunological synapse formationDOCK2, CCL19, CCL21, DLG1
5GO:0070269pyroptosisNLRC4, AIM2
5GO:0001555oocyte growthKMT2D, GDF9
5GO:0070050neuron cellular homeostasisCHRNA1, TYRO3, HAAO, FGGY
5GO:0031577spindle checkpointSPDL1, BIRC5, TAOK1
4GO:0000320re-entry into mitotic cell cycleGSK3B, CCNF, CCND1
5GO:0033206meiotic cytokinesisACTR3, ACTR2
4GO:0007127meiosis IPSMD13, CKS2
5GO:0051322anaphaseCUL3, USP44
5GO:0007109cytokinesis, completion of separationSPAST, ANXA11
5GO:0034088maintenance of mitotic sister chromatid cohesionNIPBL, DSCC1, RB1, MAU2
4GO:0044770cell cycle phase transitionTIPIN, TIMELESS, CDC7, PTPRC
4GO:0045023G0 to G1 transitionMDM4, CDK3
4GO:0051304chromosome separationSMARCAD1, RECQL5
5GO:0051306mitotic sister chromatid separationTEX14, DIS3L2
5GO:0051653spindle localizationACTR3, ACTR2, WASL
4GO:0070314G1 to G0 transitionEZH2, CYP27B1, C2orf40
5GO:0070315G1 to G0 transition involved in cell differentiationSLC39A5, CAPN3
4GO:0048278vesicle dockingEXOC5, CAV2, CCDC41
5GO:0043241protein complex disassemblyDDIT4, HDAC6
3GO:0030029actin filament-based processELMO1, SELE
5GO:0006930substrate-dependent cell migration, cell extensionOPHN1, SDCBP, MYH10, CD2AP
5GO:0030035microspike assemblyACTN2, FGD4, MTSS1
4GO:0032796uropod organizationCORO1A, MYH9
5GO:0044375regulation of peroxisome sizePEX11G, PEX11A, PEX11B
4GO:0043482cellular pigment accumulationSHROOM3, SHROOM2
5GO:0002934desmosome organizationDSP, PERP, PVRL1
3GO:0035845photoreceptor cell outer segment organizationAHI1, RP1, TOPORS, NPHP1
5GO:0071711basement membrane organizationFSHR, RIC8A, TFAP2A
4GO:0097062dendritic spine maintenancePICK1, TANC1, MTMR2
5GO:0007501mesodermal cell fate specificationHOXA11, EYA2, PAX2, SIX2
5GO:0048866stem cell fate specificationSOX18, SOX17
5GO:0007403glial cell fate determinationNTF3, CTNNB1, SMARCA4
5GO:0007493endodermal cell fate determinationSOX17, GATA6
5GO:0007500mesodermal cell fate determinationKLF4, BMP4, TRIM15, TDGF1P3
5GO:0007518myoblast fate determinationIFRD1, MYOD1
5GO:0007521muscle cell fate determinationTBX2, MEF2C, MEF2A
5GO:0048664neuron fate determinationWNT1, LBX1, CDC42
5GO:0060913cardiac cell fate determinationMESP1, ISL1, POU5F1, SOX17
5GO:0001826inner cell mass cell differentiationNLE1, TET1, HNF1B
5GO:0009994oocyte differentiationKMT2B, NPM2
5GO:0010668ectodermal cell differentiationERF, VPS52
5GO:0021533cell differentiation in hindbrainPHOX2B, NOG, FOXA2, GATA2
5GO:0021979hypothalamus cell differentiationOTP, POU3F2, PROP1
5GO:0035987endodermal cell differentiationNODAL, HMGA2, MIXL1
5GO:0035990tendon cell differentiationTNMD, BMP4, MKX, SCXA
5GO:0048333mesodermal cell differentiationHMGA2, KDM6A, INHBA
5GO:0060126somatotropin secreting cell differentiationWNT4, PITX2, PROP1
5GO:0060128corticotropin hormone secreting cell differentiationFGF8, FGF2, BMP2
5GO:0060290transdifferentiationPDX1, SMAD3, CD34
5GO:0060591chondroblast differentiationRARA, FGF4, FGF2, CYR61
5GO:0060718chorionic trophoblast cell differentiationMAP3K4, DNMT3L, E2F7, E2F8
5GO:0003329pancreatic PP cell fate commitmentNEUROD1, NKX2-2
5GO:0014034neural crest cell fate commitmentSFRP1, WNT8A
5GO:0021781glial cell fate commitmentNRG1, HES5, SOX2
5GO:0035854eosinophil fate commitmentGATA2, GATA1
5GO:0048625myoblast fate commitmentPITX1, TCF7L2, EPAS1
5GO:0072560type B pancreatic cell maturationNKX6-1, RFX3
5GO:0051124synaptic growth at neuromuscular junctionLRP4, APP
4GO:0007529establishment of synaptic specificity at neuromuscular junctionCHAT, GPHN, F2R
4GO:0060074synapse maturationSHANK1, PALM, PTEN
4GO:0008356asymmetric cell divisionPARD3, ACTR3, ACTR2
5GO:0010070zygote asymmetric cell divisionRGS14, DICER1
4GO:0021869forebrain ventricular zone progenitor cell divisionPOU3F3, POU3F2, DIXDC1
5GO:0032418lysosome localizationHDAC6, LAMTOR1, VPS33B, VPS33A
5GO:0051646mitochondrion localizationMFN2, MUL1
5GO:0051647nucleus localizationDMD, CAV3
5GO:0051648vesicle localizationTPGS1, MYO1A
4GO:0051668localization within membraneCDH13, RAC1, CNIH2
5GO:0008298intracellular mRNA localizationCASC3, STAU1, BICD1
5GO:0006880intracellular sequestering of iron ionFTH1, SRI
5GO:0023041neuronal signal transductionNLGN1, P2RY11, NRXN1
5GO:0097527necroptotic signaling pathwayRIPK1, TNF, TLR3, FASLG
5GO:0070417cellular response to coldFOXO1, NFKBIA
5GO:0071470cellular response to osmotic stressPKD2, TRPV4, DDX3X, SLC2A4
4GO:0043503skeletal muscle fiber adaptationMYOD1, ACTA1
5GO:0071453cellular response to oxygen levelsMYOD1, LPAR1, UCK2
5GO:0071467cellular response to pHKCNK18, GPLD1, HYAL1
5GO:0071219cellular response to molecule of bacterial originIRG1, FZD5
5GO:0071226cellular response to molecule of fungal originCLEC7A, SYK
3GO:0060242contact inhibitionPTPRJ, TSPO, YAP1
3GO:0060352cell adhesion molecule productionGCNT1, GOLPH3
3GO:0072553terminal button organizationNLGN2, NLGN1, SNAPIN
3GO:0097061dendritic spine organizationPICK1, ARF1
5GO:0019043establishment of viral latencyCREB3, IRF7
5GO:0019046release from viral latencyCREB3, HCFC1
5GO:0019076viral release from host cellPPID, PPIA, IST1
5GO:0046755viral buddingTSG101, LRSAM1
4GO:0043163cell envelope organizationTGM1, TGM3
5GO:0002176male germ cell proliferationDMRT1, EIF2S2, SPINK2
1GO:0022414reproductive processANTXR1, ANTXR2
4GO:0001547antral ovarian follicle growthGPR149, FOXO3, ESR1
4GO:0046661male sex differentiationDMRT1, FKBP4
3GO:0022601menstrual cycle phaseSFRP1, SFRP4, TGFB2, TGFB3
3GO:0043084penile erectionEDNRA, AVP, ACVR2A, AVPR1A
3GO:0007320inseminationP2RX1, TAC1, SEMG1, DDO
4GO:0007620copulationABAT, PI3
4GO:0051856adhesion to symbiontICAM1, SCARB1, PVRL2
1GO:0023052signalingCCR5, CCL3
4GO:0043932ossification involved in bone remodelingTGFB1, TGFB3, CTHRC1
4GO:0010573vascular endothelial growth factor productionGPR56, HIF1A
4GO:0032602chemokine productionS100A9, S100A8
5GO:0071954chemokine (C-C motif) ligand 11 productionCXCR3, TNFSF4
5GO:0032608interferon-beta productionTMEM173, TRIM56, IRF7
5GO:0032611interleukin-1 beta productionIL1B, MR1, PYCARD, CASP1
4GO:0032623interleukin-2 productionSLC11A1, STOML2
4GO:0032633interleukin-4 productionTXK, ITK
3GO:0002532production of molecular mediator involved in inflammatory responseIL4R, CHIA
4GO:0002537nitric oxide production involved in inflammatory responseSLC7A2, TLR4
5GO:0002540leukotriene production involved in inflammatory responseALOX5AP, ALOX5
4GO:0003012muscle system processTRIM72, SCO2
5GO:0060073micturitionKCNMA1, ADRA1A
5GO:0070293renal absorptionSLC9A3R1, HBB, AKR1C3
5GO:0001976neurological system process involved in regulation of systemic arterial blood pressureDRD2, MECP2, CALCA
5GO:0010159specification of organ positionHOXA3, BMP4, FOXH1, TBX3
5GO:0021532neural tube patterningPTCH1, RPGRIP1L, TMEM107
5GO:0021796cerebral cortex regionalizationEMX2, EMX1, PAX6
5GO:0021871forebrain regionalizationWNT7B, LHX1, PGAP1, WNT2B
5GO:0021978telencephalon regionalizationLHX2, BMP4, BMP2, SHH
4GO:0009798axis specificationWNT6, APC
5GO:0009855determination of bilateral symmetryALDH1A2, RALDH2
4GO:0065001specification of axis polarityAHI1, BCOR
5GO:0010085polarity specification of proximal/distal axisNODAL, WNT8A
4GO:0044241lipid digestionPNLIP, CEL, CLPS, PNLIPRP2
5GO:0042637catagenTGFB2, BARX2
5GO:0048820hair follicle maturationERCC2, RBPJ
4GO:0032902nerve growth factor productionPCSK6, FURIN
4GO:0042596fear responseADRA2A, DRD4, DBH, ADRB1
3GO:0034381plasma lipoprotein particle clearanceMSR1, CD36
4GO:0034447very-low-density lipoprotein particle clearanceAPOC1, APOE, VLDLR
4GO:0060437lung growthRSPO2, SPRY2
4GO:0042633hair cyclePTCH2, PPP1R13L, MPZL3, SNRPE
4GO:0002248connective tissue replacement involved in inflammatory response wound healingTGFB1, HIF1A, F2R
4GO:0003294atrial ventricular junction remodelingGJA1, GJA5
4GO:0048871multicellular organismal homeostasisPPP1R13L, TENC1, NDN
3GO:0050878regulation of body fluid levelsPDSS2, HEG1, EPHB2
5GO:0050882voluntary musculoskeletal movementHIPK2, ITPR1
5GO:0050883musculoskeletal movement, spinal reflex actionDRD3, CACNA1A
4GO:0007509mesoderm migration involved in gastrulationEPB41L5, T
5GO:0042249establishment of planar polarity of embryonic epitheliumFOXF2, CELSR1
4GO:0060197cloacal septationTP63, BMP4, WNT11
3GO:0035922foramen ovale closureTBX20, GJA5
2GO:0009838abscissionSPG20, IST1
5GO:0061042vascular wound healingMCAM, CD34, HPSE
4GO:0001705ectoderm formationLHX1, FOXA2
5GO:0048320axial mesoderm formationEPHA2, AXIN1
5GO:0048341paraxial mesoderm formationHTT, LEF1, HNF1A, FOXC1
3GO:0003188heart valve formationSOX9, SCXA
4GO:0003190atrioventricular valve formationSMAD4, HEY1
4GO:0003192mitral valve formationNOTCH1, ZFPM1
4GO:0003193pulmonary valve formationTBX20, GJA5
4GO:0003195tricuspid valve formationZFPM1, HEY2
3GO:0003207cardiac chamber formationNOTCH1, TBX20
5GO:0003218cardiac left ventricle formationHAND1, TBX5
5GO:0003219cardiac right ventricle formationNOTCH1, HAND1, HAND2, SMARCD3
3GO:0003272endocardial cushion formationTBX20, BMPR1A
4GO:0010260organ senescencePDX1, CTGF
5GO:0032289central nervous system myelin formationERCC2, TENM4
5GO:0032290peripheral nervous system myelin formationDICER1, NCMAP
3GO:0014028notochord formationEPHA2, T, EFNA1
3GO:0021508floor plate formationSMO, FOXH1, GLI2
4GO:0021623oculomotor nerve formationPHOX2A, TFAP2A
5GO:0021722superior olivary nucleus maturationCDK5R1, CDK5R2
5GO:0070977bone maturationGH1, FGFR3
5GO:0034505tooth mineralizationCOL1A1, AMELX
5GO:0001838embryonic epithelial tube formationWNT4, SHANK3, RET
3GO:0035802adrenal cortex formationCITED2, WT1
4GO:0048069eye pigmentationLEF1, HPS1
4GO:0021589cerebellum structural organizationDAB1, HSPA5
5GO:0021612facial nerve structural organizationHOXA1, EGR2, HOXB2, HOXB1
5GO:0021633optic nerve structural organizationKCNA2, PAX2
4GO:0001832blastocyst growthZNF830, UBTF, NBN, SMARCA4
4GO:0048630skeletal muscle tissue growthCHRNA1, IGFBP5, CHRND
5GO:0072092ureteric bud invasionSALL1, KIF26B
4GO:0060440trachea formationBMP4, TGFBR2, CTNNB1
4GO:0060914heart formationSOX17, BMPR1A
3GO:0048859formation of anatomical boundaryNODAL, SMAD4, SHH, GDF3
3GO:0060033anatomical structure regressionWNT7B, CD248, LEF1, SPI1
4GO:0060032notochord regressionGLI2, GLI1
3GO:0060061Spemann organizer formationWNT1, FZD5
3GO:0060214endocardium formationOVOL2, SOX18, SOX17, PROX1
3GO:0060661submandibular salivary gland formationFGF10, CDC42
5GO:0046619optic placode formation involved in camera-type eye formationFRS2, PROX1
4GO:0030910olfactory placode formationAXIN1, SOX2, POU2F1, PROX1
4GO:0060596mammary placode formationLRP6, TBX2, NRG3, TBX3
3GO:0060900embryonic camera-type eye formationSTRA6, TWIST1
3GO:0072033renal vesicle formationWNT4, CTNNB1
3GO:0072104glomerular capillary formationNOTCH3, BMP4
4GO:0072277metanephric glomerular capillary formationTCF21, PDGFRB, PDGFRA
3GO:0072179nephric duct formationPAX2, GATA3
4GO:0044117growth of symbiont in hostPGLYRP3, PGLYRP2, PGLYRP1, PGLYRP4
2GO:0033058directional locomotionGRIN2C, GRIN2A, ARPIN
3GO:0003419growth plate cartilage chondrocyte proliferationCER1, NPPC
3GO:0014009glial cell proliferationLGI4, SOX11, SOX4, PTK2B
4GO:0014010Schwann cell proliferationCTNNB1, NF2
4GO:0048659smooth muscle cell proliferationEDNRA, AGT, NAA35
3GO:0033687osteoblast proliferationLRRC17, OSR2, JUNB, FIGNL1
3GO:0035726common myeloid progenitor cell proliferationUNCX, GSTP1, FLT3
3GO:0048144fibroblast proliferationWNT7B, EDNRA, SP2, AGT
5GO:0060750epithelial cell proliferation involved in mammary gland duct elongationTFAP2C, WNT5A, MED1, ESR1
3GO:0051450myoblast proliferationIGF1, MET, HGF, GPX1
4GO:0033278cell proliferation in midbrainFZD3, FZD6
4GO:0002158osteoclast proliferationNPR3, CSF1, TNFSF11
4GO:0032943mononuclear cell proliferationACE, TGFB1
4GO:0010463mesenchymal cell proliferationHAND2, FGF7, FGF4
2GO:0016265deathSLC18A2, TCF15, NR4A2
3GO:0001543ovarian follicle ruptureNRIP1, AGT
3GO:0001546preantral ovarian follicle growthGPR149, AMH
3GO:0001550ovarian cumulus expansionEREG, BMPR1B
3GO:0001554luteolysisMMP19, CASP2
3GO:0060112generation of ovulation cycle rhythmKISS1, NPY5R
5GO:0045475locomotor rhythmKCNMA1, NPAS2, NAGLU, PTEN
5GO:0015993molecular hydrogen transportSLC23A2, ADHFE1
5GO:0043490malate-aspartate shuttleSLC25A13, SLC25A12
5GO:0015918sterol transportABCG5, ABCG8, NPC1L1
5GO:0015920lipopolysaccharide transportLBP, SCARB1
4GO:0015697quaternary ammonium group transportSLC22A5, SLC22A3, SLC22A4
4GO:0015837amine transportAQP9, SLC22A16, RHCG
4GO:0015851nucleobase transportSLC23A2, SLC23A1
5GO:0048227plasma membrane to endosome transportSORT1, RAB11A
5GO:1990126retrograde transport, endosome to plasma membraneMICALL1, RAB11B, SNX27
4GO:0030185nitric oxide transportAQP1, EDN1, HBB
5GO:0032066nucleolus to nucleoplasm transportNOC2L, WRN, TBRG1
4GO:0035526retrograde transport, plasma membrane to GolgiUSP6NL, RAB43
5GO:0042045epithelial fluid transportEDN1, EDNRB, SLC26A6, CSF2
5GO:0046717acid secretionDRD2, DRD3, SLC22A16
5GO:0046967cytosol to ER transportTAP1, TAP2
5GO:0015889cobalamin transportGIF, TCN1, TCN2, CUBN
4GO:0070633transepithelial transportCXADR, SLC26A6, GPLD1
4GO:0071985multivesicular body sorting pathwayRAB27A, RAB27B, SYTL4, EXPH5
5GO:0034436glycoprotein transportABCG1, VLDLR
5GO:0001941postsynaptic membrane organizationCHRNB1, GDNF
5GO:0010256endomembrane system organizationARFGEF1, ARFGEF2
5GO:0031579membrane raft organizationPPT1, CAV3, DLG1
5GO:0033292T-tubule organizationCAV3, ANK2
5GO:0045161neuronal ion channel clusteringMTCH1, PICK1
5GO:0048499synaptic vesicle membrane organizationAP3D1, SYP
5GO:0071709membrane assemblySPTBN1, ANK3
5GO:0071763nuclear membrane organizationTOR1A, TOR1B, TOR1AIP1
5GO:0097035regulation of membrane lipid distributionTRIAP1, PRELID1
5GO:0042745circadian sleep/wake cycleTH, NPAS2
4GO:0002357defense response to tumor cellPRF1, PLK5
5GO:0002215defense response to nematodeEPX, TNFSF4
5GO:0010193response to ozoneSCGB1A1, CYP2E1, NGF, TACR1
5GO:0071731response to nitric oxideCCL19, EGLN1, CCR7
4GO:0001306age-dependent response to oxidative stressSOD2, CLN8, COQ7
5GO:0006982response to lipid hydroperoxideAPOA4, GPX3
3GO:0006991response to sterol depletionLYN, INSIG1
5GO:0009414response to water deprivationTH, CD9
5GO:0002246wound healing involved in inflammatory responseHMOX1, CD44
5GO:0034059response to anoxiaOXTR, CTGF
3GO:0035902response to immobilization stressCRHR1, TPH1, CRH, UCN3
5GO:0051788response to misfolded proteinF12, HDAC6, CLU
3GO:0051409response to nitrosative stressADH5, GCLM, GCLC, DUSP6
5GO:0051599response to hydrostatic pressureKRT8, NTRK1
5GO:0002023reduction of food intake in response to dietary excessNMUR2, PRLH
5GO:0009583detection of light stimulusPDE6B, OPN3
4GO:0009590detection of gravityOTOP1, NOX3
4GO:0016048detection of temperature stimulusNGFR, DRGX
5GO:0035995detection of muscle stretchTCAP, CSRP3, TTN
5GO:0050974detection of mechanical stimulus involved in sensory perceptionSERPINE2, ASIC2
4GO:0010996response to auditory stimulusNTRK2, CXCL10, TACR1
4GO:0035994response to muscle stretchTCAP, ANKRD1
3GO:0009991response to extracellular stimulusRASGRP4, RPS19, ACTA1
4GO:0060005vestibular reflexNR4A3, TMC1, TMC2
4GO:0097195pilomotor reflexHPN, ADRA1A, NPNT
4GO:0002238response to molecule of fungal originMYD88, TLR2
3GO:0009595detection of biotic stimulusNLRP3, NOD1, NOD2
4GO:0001562response to protozoanVTCN1, SPN, IER3
5GO:0009609response to symbiotic bacteriumGPX1, GPX2
5GO:0009597detection of virusIFIH1, DDX58, TLR3
5GO:0001878response to yeastNCF1, MPO, ELANE, PTX3
4GO:0009624response to nematodeIL25, CYP1A1, ITLN1
4GO:0071502cellular response to temperature stimulusHTR1B, HTR2B
4GO:0010447response to acidityGPR65, SLC9A1
5GO:0009642response to light intensitySLC24A1, GNAT1, GNAT2
5GO:0009648photoperiodismNMU, CLOCK
3GO:0009582detection of abiotic stimulusNPFFR2, TAC1, TIMELESS, TACR1
4GO:0014878response to electrical stimulus involved in regulation of muscle adaptationRPS6KB1, TRIM63, MYOG
4GO:0003032detection of oxygenSOD2, CYB5R4, SLC11A2
5GO:0044321response to leptinNR1D1, STAR
5GO:0097066response to thyroid hormoneHPN, AK2
4GO:0003127detection of nodal flowPKD2, PKD1L1
5GO:0034776response to histamineDRD4, DRD2, DRD3
5GO:0046898response to cycloheximideBCL2L1, GHR
5GO:0097338response to clozapinePRKAR2B, PRKACB
5GO:0055098response to low-density lipoprotein particleABCA1, SREBF2, PPARG
5GO:0055099response to high density lipoprotein particleADAM17, ABCG1
4GO:0014873response to muscle activity involved in regulation of muscle adaptationAGT, MYOG
2GO:0014854response to inactivityDRD2, IL10
3GO:0009593detection of chemical stimulusDRGX, UGT2A1
5GO:0050968detection of chemical stimulus involved in sensory perception of painASIC3, TRPA1
5GO:0046684response to pyrethroidSCN1B, TH, SCN2B, DDC
4GO:0060992response to fungicideGRIN1, CYP17A1, STAR, CYP11A1
5GO:0043331response to dsRNAPMAIP1, PELI1
5GO:0070669response to interleukin-2CITED1, STAT5B, JAK3
5GO:0070671response to interleukin-12RIPK2, JAK2
5GO:0070672response to interleukin-15STAT5B, JAK3, ACSL4
5GO:0070741response to interleukin-6CITED1, CHI3L1, SFTPC, FOXA2
5GO:0071104response to interleukin-9CITED1, JAK3
4GO:0034465response to carbon monoxideEGR1, KCNMA1, IL10
4GO:0046683response to organophosphorusTYMS, RFC3, AKR1C1, TRIM16
5GO:0010044response to aluminum ionMAOB, QDPR, LONP1
5GO:0032025response to cobalt ionD2HGDH, CASP8
4GO:0010157response to chloratePTCH1, PDX1
4GO:0034021response to silicon dioxideSOD2, SCGB1A1
3GO:0050906detection of stimulus involved in sensory perceptionPPEF2, PPEF1
4GO:0008105asymmetric protein localizationSCRIB, WNT7A, COLQ, DYNC2H1
5GO:0045175basal protein localizationNCKAP1, ERBB2IP
4GO:0031503protein complex localizationKIF17, BIRC5, DNMT3B, FKBP4
5GO:0071896protein localization to adherens junctionSCRIB, DSP, MPP7
3GO:1901998toxin transportSLC17A3, LRP6, ABCG1, SLC7A8
5GO:0071169establishment of protein localization to chromatinCCDC101, LRWD1
3GO:0051303establishment of chromosome localizationNDE1, BIRC5
4GO:0051310metaphase plate congressionCENPF, SPICE1
5GO:0032401establishment of melanosome localizationRAB17, SHROOM2
5GO:0051877pigment granule aggregation in cell centerMKKS, BBS4, BBS7
3GO:0051654establishment of mitochondrion localizationPVRL2, FEZ1
3GO:0051683establishment of Golgi localizationARHGAP21, COPG1, CDC42
2GO:0009405pathogenesisTMEM181, MECP2, CARM1
3GO:0051702interaction with symbiontGPX1, GPX2
5GO:0002920regulation of humoral immune responseCD37, SPNS2, CXCL13
3GO:0006808regulation of nitrogen utilizationBCL2, BAX
5GO:0009890negative regulation of biosynthetic processGCHFR, GSTP1
5GO:0060267positive regulation of respiratory burstINSR, CAMK1D, INS
4GO:0032350regulation of hormone metabolic processFSHR, TCF7L2
4GO:0060263regulation of respiratory burstRAC2, RAC1, NOXO1, NOXA1
5GO:0051712positive regulation of killing of cells of other organismNOS2, IFNG, FCER2
5GO:0031652positive regulation of heat generationSLC27A1, APLN
5GO:2000189positive regulation of cholesterol homeostasisNR1D1, ACOX1, NR1H3, HNF4A
5GO:2000507positive regulation of energy homeostasisSGIP1, PPARGC1A
5GO:0003254regulation of membrane depolarizationFHL1, NEDD4L, RANGRF
5GO:0061088regulation of sequestering of zinc ionSLC30A8, SLC30A4, SLC30A3, AP3D1
4GO:2000188regulation of cholesterol homeostasisNR1D1, SREBF2, FGFR4
5GO:0060178regulation of exocyst localizationRALB, RALGAPA2, RALGAPB
5GO:0060632regulation of microtubule-based movementIGBP1, MAPT, HDAC6
5GO:0001560regulation of cell growth by extracellular stimulusKIF26A, PPP1R9B, MYOCD
4GO:0040009regulation of growth ratePARP1, WRN, BNIPL
5GO:0060420regulation of heart growthDUSP6, MYH6
4GO:0042753positive regulation of circadian rhythmBTRC, FBXW11
5GO:0060406positive regulation of penile erectionEDNRB, OXT, OXTR, P2RY1
5GO:0033623regulation of integrin activationFBLIM1, FARP2, SELP
5GO:0060491regulation of cell projection assemblyCCL19, FAM110C
4GO:0090083regulation of inclusion body assemblySNCAIP, BAG5
5GO:0090084negative regulation of inclusion body assemblySACS, HSPA1A, DNAJB2
5GO:1900106positive regulation of hyaluranon cable assemblyHAS3, BMP7, HYAL1
4GO:1901888regulation of cell junction assemblyRAPGEF1, RAPGEF2, RAP1B, RAP1A
5GO:0043243positive regulation of protein complex disassemblyTNF, MGEA5, BNIP3
5GO:0050867positive regulation of cell activationJAK2, CTGF
5GO:0090343positive regulation of cell agingLMNA, TP53
5GO:0060760positive regulation of response to cytokine stimulusTAF9, WNT5A
5GO:0010902positive regulation of very-low-density lipoprotein particle remodelingAPOC2, APOA5
5GO:0060279positive regulation of ovulationPLAT, INHBA, INHBB
5GO:0010716negative regulation of extracellular matrix disassemblyCST3, FAP, DPP4
5GO:0043242negative regulation of protein complex disassemblySLN, TNF, HDAC6, IRAK3
5GO:0051782negative regulation of cell divisionPTCH1, TXNIP, BLM, MYC
5GO:0090288negative regulation of cellular response to growth factor stimulusCASK, SLIT2
5GO:2000360negative regulation of binding of sperm to zona pellucidaASTL, ZP3, ZP4
5GO:0010903negative regulation of very-low-density lipoprotein particle remodelingAPOC3, APOA1, APOA2
5GO:0050819negative regulation of coagulationPROCR, HS3ST5, ANXA5, ANXA4
5GO:1900222negative regulation of beta-amyloid clearanceLRPAP1, SRF, MYOCD
5GO:0047484regulation of response to osmotic stressMLC1, TRPV4, GYPA
5GO:0061041regulation of wound healingPLAU, VIL1
4GO:2001023regulation of response to drugADIRF, GABRA4
5GO:2001038regulation of cellular response to drugNCOA1, HMGA2
5GO:0010453regulation of cell fate commitmentFGFR2, PAX7
5GO:0051147regulation of muscle cell differentiationSUPT6H, CAMK1, MEGF10
5GO:0010649regulation of cell communication by electrical couplingCASQ2, TRDN, ASPH, SRI
5GO:1901214regulation of neuron deathRILPL1, SARM1, DHCR24
4GO:0032878regulation of establishment or maintenance of cell polarityIGF1, LLGL2, TEK
4GO:0032970regulation of actin filament-based processPARD3, CNN2, FRMD6
5GO:0090170regulation of Golgi inheritanceMAPK3, MAPK1, MAP2K2, MAP2K1
5GO:1900063regulation of peroxisome organizationMAVS, DNM1L, MFF
5GO:0014842regulation of satellite cell proliferationPAXBP1, CFLAR, ANGPT1, MYOG
5GO:0033688regulation of osteoblast proliferationRHOA, NPR3, FGFR2
5GO:0072091regulation of stem cell proliferationAGO3, SOX18, SOX17, YAP1
5GO:2000254regulation of male germ cell proliferationRHBDD1, RSPO1
5GO:0051823regulation of synapse structural plasticityCAMK2B, CTNNA2, NCAN, DMPK
5GO:0009786regulation of asymmetric cell divisionPOU5F1, WNT9B
5GO:2000035regulation of stem cell divisionSFRP2, SOX17
4GO:0060968regulation of gene silencingHIST1H3A, CDK2
5GO:2000327positive regulation of ligand-dependent nuclear receptor transcription coactivator activityRQCD1, CNOT6
5GO:0032649regulation of interferon-gamma productionRIPK3, ISG15, CCR7
5GO:0032675regulation of interleukin-6 productionMAPKAPK2, HLA-B, AFAP1L2
5GO:0032680regulation of tumor necrosis factor productionMAPKAPK2, TBC1D23, ZFP36, LTF
5GO:0034344regulation of type III interferon productionIFIH1, DDX58
5GO:0010988regulation of low-density lipoprotein particle clearanceHNRNPK, CNPY2, FGF21
4GO:0034103regulation of tissue remodelingCST3, TP53, THBS4
5GO:0046850regulation of bone remodelingINPP4B, SUCO, GJA1
4GO:0042634regulation of hair cycleNIPBL, FA2H
5GO:0044065regulation of respiratory system processMTG2, MTG1, FTO
3GO:0051917regulation of fibrinolysisAPOH, FAP
3GO:0097006regulation of plasma lipoprotein particle levelsLPCAT3, DGAT2
3GO:1900271regulation of long-term synaptic potentiationNLGN3, SHANK3
4GO:0080154regulation of fertilizationRNASE10, ASUN, PLCB1
3GO:0001505regulation of neurotransmitter levelsZNF219, GABRA2, PDE1B, DVL1
4GO:0014916regulation of lung blood pressureGCH1, BMPR2
5GO:0003085negative regulation of systemic arterial blood pressureNEDD4L, IER3, BBS4, BMPR2
3GO:0010817regulation of hormone levelsBCAT2, FOXA3, FOXA2, SOX8
5GO:0045759negative regulation of action potentialCNR1, CNR2, CHRNB2
5GO:0086001regulation of cardiac muscle cell action potentialDMD, PKP2
5GO:0010917negative regulation of mitochondrial membrane potentialPMAIP1, PRELID1
4GO:0045838positive regulation of membrane potentialPIAS3, ANK3, GIMAP5
5GO:0010918positive regulation of mitochondrial membrane potentialSTOML2, BAD
5GO:0086010membrane depolarization involved in regulation of action potentialYWHAH, SCN3B, KCNH2, SCN5A
4GO:0060075regulation of resting membrane potentialKCNJ10, PSEN1, KCNJ2
4GO:0086036regulation of cardiac muscle cell membrane potentialATP2A2, TRDN, EHD3, PLN
5GO:0030104water homeostasisIGF1, AQP9, NEDD4L, GHRHR
5GO:0050801ion homeostasisWNK4, KLHL3, AMELX, CRH
3GO:0050803regulation of synapse structure and activityPPT1, APP, SYNGAP1
5GO:0030730sequestering of triglycerideIL1B, TNF, ENPP1
5GO:0032119sequestering of zinc ionS100A9, S100A8, SLC30A8, SLC30A7
5GO:0051208sequestering of calcium ionATP7B, CALR, CASQ2, HSP90B1
5GO:0035565regulation of pronephros sizeHNF1B, HNF1A
5GO:0035566regulation of metanephros sizePAX2, AGTR2
3GO:0040030regulation of molecular function, epigeneticASIP, CTCF
4GO:0051100negative regulation of bindingCYP2D6, YBX2, P2RY1
5GO:0035562negative regulation of chromatin bindingTDG, WAPAL, MEPCE, SENP2
5GO:1901877negative regulation of calcium ion bindingSLN, PLN
5GO:0001845phagolysosome assemblyP2RX7, SRPX, CORO1A, MYO7A
4GO:0010324membrane invaginationFCHO2, FNBP1L
4GO:0016557peroxisome membrane biogenesisPEX11A, PEX19, PEX16, PEX3


 


 

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