WormMine: Gene WBGene00003911

• WormBase Gene ID: WBGene00003911
• Gene Name: pak-1
• Sequence Name: C09B8.7
• Brief Description: pak-1 encodes, by alternative splicing, at least five isoforms of aputative p21-activated kinase orthologous to human PAK1, PAK2 (OMIM:?),and PAK3 (OMIM:300142, mutated in nonsyndromic mental retardation);PAK-1 is required (redundantly with its paralog, MAX-2) for normalaxonal guidance of motoneurons, P cell migration, and locomotion, withmax-2(cy2);pak-1(ok448) double mutants phenotypically resembling unc-73or ced-10;mig-2 mutants; pak-1 is expressed in pharyngeal muscles, CANneurons, ventral cord motoneurons, migrating distal tip cells,developing uterus, B, Y, and T cells in the male tail, and vulval musclecells; by itself, the null pak-1(ok448) mutation has no known phenotype.
• Organism: Caenorhabditis elegans
• Automated Description: Enables GTP binding activity and protein kinase activity. Involved in several processes, including anatomical structure morphogenesis; hemidesmosome assembly; and inductive cell migration. Located in several cellular components, including axon; hemidesmosome; and neuronal cell body. Expressed in several structures, including P5.p hermaphrodite; P7.p hermaphrodite; gonad; hypodermis; and neurons. Human ortholog(s) of this gene implicated in several diseases, including Alzheimer's disease; carcinoma (multiple); kidney cancer (multiple); and non-syndromic X-linked intellectual disability 30. Is an ortholog of human PAK1 (p21 (RAC1) activated kinase 1); PAK2 (p21 (RAC1) activated kinase 2); and PAK3 (p21 (RAC1) activated kinase 3).
• Biotype: SO:0001217
• Genetic Position: X :-3.80222 ±0.008236
• Length (nt): 4301

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003911

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C09B8.7b.1	C09B8.7b.1	2304	X: 6044308-6048606
Transcript:C09B8.7a.1	C09B8.7a.1	2314	X: 6044309-6048608
Transcript:C09B8.7c.1	C09B8.7c.1	1572	X: 6044894-6048301

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C09B8.7a	C09B8.7a	1719	X: 6044894-6045052
CDS:C09B8.7b	C09B8.7b	1710	X: 6044894-6045052
CDS:C09B8.7c	C09B8.7c	1572	X: 6044894-6045052

16 RNAi Result

• WBRNAi00083108
• WBRNAi00102023
• WBRNAi00102019
• WBRNAi00102025
• WBRNAi00102027
• WBRNAi00102026
• WBRNAi00040162
• WBRNAi00028710
• WBRNAi00109205
• WBRNAi00109400
• WBRNAi00109303
• WBRNAi00109594
• WBRNAi00109497
• WBRNAi00116140
• WBRNAi00010509
• WBRNAi00083096

77 Allele

• gk964260
• WBVar01926876
• WBVar01926877
• gk751691
• gk720050
• WBVar00079614
• WBVar02027168
• WBVar01980765
• WBVar01880616
• tm11128
• gk281951
• tm403
• gk962610
• gk585510
• gk644975
• gk450226
• gk851241
• gk846904
• gk644976
• gk666261
• gk484738
• gk487809
• gk906891
• gk841969
• gk894286
• gk698967
• gk597975
• gk679428
• gk657579
• gk726094

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003911
• Start: 6044308
• End: 6048608
• Strand: -1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrX_6041093..6044307
• Length (nt): 3215
• Chromosome Location: X: 6041093-6044307
• Organism: Caenorhabditis elegans

126 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
adult vs dauer larva	Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C.	N.A.	WBPaper00050488:adult_vs_dauer_regulated_N2_20C
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_expressed
	Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva and Late reproduction stage (96 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_regulated_developing
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
	Transcripts that showed significantly increased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs
	Transcripts that showed significantly increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_upregulated
	Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
	Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours.	The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data.	WBPaper00065373:Cisplatin_downregulated_WT
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_upregulated
	Transcripts that showed significantly altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain.	RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis.	WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR
	Genes significantly enriched (> 2x, FDR < 5%) in a particular cell-type versus a reference sample of all cells at the same stage.	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:hypodermis_larva_enriched
	Transcripts that showed significantly increased expression in dpy-21(e428) comparing to in N2 during L3 stage.	DESeq v1.6.3. Fold change > 1.5.	WBPaper00050370:dpy-21(e428)_L3_upregulated
Fungi infection: Haptoglossa zoospora.	Transcripts that showed significantly altered expression after L4 N2 animals were exposed to omycete Haptoglossa zoospora for 6 hours.	Kalisto abundance files were converted and analysed using Sleuth in a R pipeline. Standard Sleuth protocols were used to calculate differential expression. P value < 0.01 and FDR < 0.01.	WBPaper00062354:H.zoospora_6h_regulated
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult
	Transcripts that showed significantly increased expression in pgl-1(ct131) animals (isolated from SS0002[pgl-1(ct131)him-3(e1147)], comparing to in control animals SS1174, at 1-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_pgl-1(ct131)_vs_control_day1-adult
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	Transcripts of coding genes that showed significantly increased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_enriched_coding-RNA
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes

13 Expression Patterns

• Primary Identifier: Expr1031845
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr709
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: Expression first detected in embryos though to adulthood. In L1, strong staining detected in the pharynx and in 2 laterally located cells (NLS-lacZ staining). The pharyngeal cells are muscle cells which occupy most of the body of the pharynx and the lateral cells were CAN neurons based on the position of the nucleus and axon morphology. Both pharyngeal muscle and CAN neurons express reporter as embryo through to adulthood. Also stained were several cells in the tail region. These include the B and Y cells (forming male spicule) from L1 to adult, the hypodermal blast cells T in the L1 and some of its progeny in later stages. In L1, subset of cells in ventral nerve cord and DA identified as DB neurons (cholinergic motor neurons innervating dorsal body wall muscles) stain. Cells identified by GFP: GFP without NLS revealed expression in distal tip cells (DTC) spermatheca and uterus. It is not clear if GFP is expressed by somatic cells of the gonad or by the germline cells (namely sperm) in the spermatheca. Expression in uterus was seen outside the embryos. It is not clear which cells expressed the reporter in uterus although observation of NLS-lacZ and NLS-GFP indicated that some somatic cells of the gonad expressed CePAKGFP without NLS. There is expression in many hypodermal cells surrounding the embryos during the morphogenetic stage. C-terminus two amino-acids of CePAK replaced with GFP coding sequence and fusion protein was expressed from the CePAK promoter used to analyze intracellular localization (pCPK2.77). CePAK GFP was enriched at cell surface in pharyngeal muscle cells especially condensed at cell boundaries. In CAN neurons CePAK GFP detected in cell bodies and along the axons. CePAK GFP localized to cell bodies and their processes running along the excretory canal on the lateral surface of adults.

• Primary Identifier: Expr11236
• Pattern: pak-1 is expressed in the hypodermal tissue before and during the HSN migrations, consistent with earlier PAK-1 expression pattern reports. Expression is restricted to the hypodermal tissue throughout embryogenesis beginning prior to HSN migration (bean stage) and during HSN migration (1.5-fold), and continues in the hypodermis during late embryogenesis (3-fold).

• Primary Identifier: Expr11237
• Pattern: pak- 1 expression is seen in the early embryo and continues throughout all stages of embryogenesis. Expression is highly localized to the hypodermal cells beginning in the bean stage and occurring through the 1.5-fold stage, which is consistent with the timing of HSN migration. The authors assume that these are hypodermal cells based on the pak-1 transcriptional reporter overlap with marked hypodermal cells. pak-1 expression is dramatically reduced in the 3-fold embryo and becomes restricted mainly to the CAN.

• Primary Identifier: Expr2321
• Remark: As a negative control, no signal was detected in similar immunofluorescence analysis using the CePAK antibody, which was blocked by the GST/CePAK fusion protein.
• Pattern: Whereas no signal was detected in early embryogenesis where cell proliferation takes place, CePAK was specifically localized at all hypodermal cell boundaries throughout the second phase of the embryogenesis. The identity of these cells as hypodermal cells was supported by the identical staining pattern of the MH27 monoclonal antibody, which exclusively recognizes hypodermal cell boundaries. During the elongation event, boundaries of the hypodermal cells disappear progressively as the distance between the longitudinal margins of each cell increase, whereas that between the circumferential margins decrease. The CePAK staining pattern coincided with these cell shape changes, as illustrated from an embryo at the beginning of elongation when all hypodermal cell boundaries were still present to an elongated embryo where only two continuous longitudinal boundaries were observed.
• Subcellular Localization: cell boundaries

• Primary Identifier: Expr13096
• Pattern: Refers to NEXTDB In-situ hybridization pattern in the adult gonad.

• Primary Identifier: Expr10199
• Pattern: pak-1::gfp reporter was expressed in cells previously reported to express pak-1, including CAN neurons and ventral cord motor neurons. In addition to cells previously reported to express pak-1, this reporter was expressed at a low level in P5.p, P6.p, and P7.p vulval cell lineages during the L3 and L4 stages, consistent with cell-autonomous function.
• Subcellular Localization: In most cells including P5.p and P7.p, the PAK-1::GFP fusion protein localized to the cytoplasm. No obvious membrane localization or asymmetric localization of PAK-1::GFP was observed in vulval cells.

• Primary Identifier: Expr1023648
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr14857
• Subcellular Localization: PAK-1and SPC-1 colocalize with actin filaments.

• Primary Identifier: Expr1144238
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2032919
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr1597
• Remark: pak-1 = CePAK. --wjc.
• Pattern: CePAK was highly expressed at embryonic stages, expression level decrease from L1 stage and onward.

• Primary Identifier: Expr2014686
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

45 GO Annotation

17 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003911
• Start: 6044308
• End: 6048608
• Strand: -1

45 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 4301

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00031427
• WBStrain00000137

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrX_6048609..6048626
• Length (nt): 18
• Chromosome Location: X: 6048609-6048626
• Organism: Caenorhabditis elegans