"Table S20. Significant PCB126 (PCB) treatment patterns shared by gene pathways and behavior endpoints in Scorton Creek (SCO) Atlantic killifish found in this study.  Both the original and opposite behavior endpoint trends are listed (Ctrl = Control treatment, Neg = significant negative trend compared to control, Pos = significant positive trend compared to control, NS = no significant trend compared to control, HMM = Hidden Markov Chain model endpoint, TP = Transition Probability)."							
Reference Number	Significant Treatment Pattern					Significant Treatment Pattern in a Behavior Endpoint	
	SCO-Ctrl vs SCO-PCB	 SCO-Ctrl vs NBH-Ctrl	 SCO-PCB vs NBH-PCB	 NBH-Ctrl vs NBH-PCB	Altered Gene Pathway	Original Treatment Pattern	Opposite Treatment Pattern
1	NS	NS	Pos	NS	 Neural: Neuroactive ligand-receptor interaction(KEGG 2D:4080)	"Swimming Bout Duration Period 2 (sec), Swimming Bout Duration Period 4 (sec)"	"Startle Magnitude Period 4, Swimming Bout Turning Angle Period 3"
2	NS	Neg	NS	Pos	Metabolic: Oxidative phosphorylation(KEGG:190)	"HMM Medium State Turning Angle, HMM Slow -> Medium TP"	"HMM Medium -> Medium TP, HMM Medium -> Slow TP, HMM Slow -> Slow TP"
3	NS	Neg	NS	NS	"Neural: ubiquinone metabolic process(BP-GO:0006743), proteasomal ubiquitin-independent protein catabolic process(BP-GO:0010499), NADH dehydrogenase (ubiquinone) activity(MF-GO:0008137), ubiquinone biosynthetic process(BP-GO:0006744) Nucleic: RNA polymerase(KEGG:3020), Homologous recombination(KEGG:3440), purine ribonucleotide biosynthetic process(BP-GO:0009152), pyrimidine nucleotide metabolic process(BP-GO:0006220), Nucleotide excision repair(KEGG:3420), nucleotide metabolic process(BP-GO:0009117), U2-type spliceosomal complex(CC-GO:0005684), U2 snRNP(CC-GO:0005686), nucleotide biosynthetic process(BP-GO:0009165), tRNA methyltransferase activity(MF-GO:0008175), mRNA splicing, via spliceosome(BP-GO:0000398), Cytosolic Dsensing pathway(KEGG:4623), spliceosomal complex(CC-GO:0005681), spliceosomal snRNP assembly(BP-GO:0000387), double-strand break repair via homologous recombination(BP-GO:0000724), purine nucleotide biosynthetic process(BP-GO:0006164), RNA polymerase II, core complex(CC-GO:0005665), Spliceosome(KEGG:3040), Ddirected 5'-3' RNA polymerase activity(MF-GO:0003899), recombinational repair(BP-GO:0000725), kinetochore(CC-GO:0000776), purine nucleoside triphosphate metabolic process(BP-GO:0009144), nucleoside phosphate metabolic process(BP-GO:0006753), purine nucleotide metabolic process(BP-GO:0006163), purine ribonucleoside triphosphate metabolic process(BP-GO:0009205), RNA splicing, via transesterification reactions(BP-GO:0000375), Aminoacyl-tRNA biosynthesis(KEGG:970), RNA polymerase III complex(CC-GO:0005666), metaphase/anaphase transition of mitotic cell cycle(BP-GO:0007091), Ddirected RNA polymerase complex(CC-GO:0000428), regulation of mitotic sister chromatid separation(BP-GO:0010965), RNA methyltransferase activity(MF-GO:0008173), ribonucleoside triphosphate biosynthetic process(BP-GO:0009201), tRNA processing(BP-GO:0008033), ribonucleotide biosynthetic process(BP-GO:0009260), RNA splicing(BP-GO:0008380), nucleobase metabolic process(BP-GO:0009112), mRNA processing(BP-GO:0006397), nucleoside triphosphate metabolic process(BP-GO:0009141), pyrimidine nucleotide biosynthetic process(BP-GO:0006221), purine ribonucleotide metabolic process(BP-GO:0009150), Dtemplated transcription, initiation(BP-GO:0006352), ribonucleotide metabolic process(BP-GO:0009259), RNA splicing, via transesterification reactions with bulged adenosine as nucleophile(BP-GO:0000377), ribonucleoside triphosphate metabolic process(BP-GO:0009199), tRNA modification(BP-GO:0006400) Signaling: cytochrome-c oxidase activity(MF-GO:0004129), electron transfer activity(MF-GO:0009055), copper ion binding(MF-GO:0005507), proton channel activity(MF-GO:0015252) Metabolic: Fatty acid metabolism(KEGG:1212), mitochondrial inner membrane(CC-GO:0005743), Carbon metabolism(KEGG:1200), Arachidonic acid metabolism(KEGG:590), mitochondrial respiratory chain complex I(CC-GO:0005747), mitochondrial respiratory chain complex IV(CC-GO:0005751), Glutathione metabolism(KEGG:480), mitochondrion organization(BP-GO:0007005), Pyruvate metabolism(KEGG:620), Valine, leucine and isoleucine degradation(KEGG:280), Propanoate metabolism(KEGG:640), Tryptophan metabolism(KEGG:380), fatty acid metabolic process(BP-GO:0006631), fatty acid beta-oxidation(BP-GO:0006635), mitochondrial large ribosomal subunit(CC-GO:0005762), carbohydrate catabolic process(BP-GO:0016052), organic acid biosynthetic process(BP-GO:0016053), sulfur compound metabolic process(BP-GO:0006790), organic acid metabolic process(BP-GO:0006082), iron-sulfur cluster assembly(BP-GO:0016226), Porphyrin and chlorophyll metabolism(KEGG:860), mitochondrial envelope(CC-GO:0005740), mitochondrial ribosome(CC-GO:0005761), protein targeting to mitochondrion(BP-GO:0006626), mitochondrial matrix(CC-GO:0005759), branched-chain amino acid metabolic process(BP-GO:0009081), oxidative phosphorylation(BP-GO:0006119), mitochondrial small ribosomal subunit(CC-GO:0005763), monosaccharide metabolic process(BP-GO:0005996), mitochondrial electron transport, NADH to ubiquinone(BP-GO:0006120) Stress: response to oxidative stress(BP-GO:0006979), response to stress(BP-GO:0006950), response to reactive oxygen species(BP-GO:0000302), response to biotic stimulus(BP-GO:0009607) Transport: endoplasmic reticulum to Golgi vesicle-mediated transport(BP-GO:0006888), pyrophosphate hydrolysis-driven proton transmembrane transporter activity(MF-GO:0009678), proton-transporting two-sector ATPase complex(CC-GO:0016469), proton transmembrane transporter activity(MF-GO:0015078) Cellular: membrane(CC-GO:0016020), generation of precursor metabolites and energy(BP-GO:0006091), lytic vacuole(CC-GO:0000323), organellar large ribosomal subunit(CC-GO:0000315), cytochrome complex assembly(BP-GO:0017004), Phagosome(KEGG:4145), energy derivation by oxidation of organic compounds(BP-GO:0015980), extracellular space(CC-GO:0005615), vacuolar membrane(CC-GO:0005774), cellular amino acid metabolic process(BP-GO:0006520), protein peptidyl-prolyl isomerization(BP-GO:0000413), Lysosome(KEGG:4142), organellar small ribosomal subunit(CC-GO:0000314), vacuole(CC-GO:0005773), extracellular region(CC-GO:0005576), cellular amino acid biosynthetic process(BP-GO:0008652), organellar ribosome(CC-GO:0000313), lysosome(CC-GO:0005764) Catalytic: peptidyl-prolyl cis-trans isomerase activity(MF-GO:0003755), threonine-type endopeptidase activity(MF-GO:0004298), exopeptidase activity(MF-GO:0008238), NADH dehydrogenase activity(MF-GO:0003954), oxidoreductase activity, acting on CH-OH group of donors(MF-GO:0016614), oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor(MF-GO:0016616), serine-type peptidase activity(MF-GO:0008236), ligase activity(MF-GO:0016874), oxidoreductase activity, acting on NAD(P)H(MF-GO:0016651), oxidoreductase activity, acting on a sulfur group of donors(MF-GO:0016667), disulfide oxidoreductase activity(MF-GO:0015036), oxidoreductase activity, acting on a heme group of donors(MF-GO:0016675), transferase activity, transferring alkyl or aryl (other than methyl) groups(MF-GO:0016765), lyase activity(MF-GO:0016829), isomerase activity(MF-GO:0016853), monooxygenase activity(MF-GO:0004497), oxidoreductase activity, acting on the CH-CH group of donors(MF-GO:0016627), S-adenosylmethionine-dependent methyltransferase activity(MF-GO:0008757), oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor(MF-GO:0016655), cis-trans isomerase activity(MF-GO:0016859), mannosyltransferase activity(MF-GO:0000030) Miscellaneous: proteasome core complex(CC-GO:0005839), Glycolysis / Gluconeogenesis(KEGG:10), Steroid biosynthesis(KEGG:100), proteasome regulatory particle(CC-GO:0005838), Proteasome(KEGG:3050), proteasome complex(CC-GO:0000502)"	"HMM Medium -> Fast TP, Swimming Bout Duration (sec)"	"Prey Capture Probability, Reaction DisNegce (mm), Startle Magnitude Period 2"
4	NS	Pos	NS	NS	"Neural: axon guidance(BP-GO:0007411), axonogenesis(BP-GO:0007409), postsynaptic density(CC-GO:0014069), glial cell differentiation(BP-GO:0010001), neural crest cell development(BP-GO:0014032), dopamine receptor signaling pathway(BP-GO:0007212), neuron recognition(BP-GO:0008038), regulation of neuron projection development(BP-GO:0010975), peripheral nervous system development(BP-GO:0007422), central nervous system development(BP-GO:0007417), neural crest cell differentiation(BP-GO:0014033), ubiquitin-protein transferase activity(MF-GO:0004842), synaptic vesicle(CC-GO:0008021), negative regulation of neuron projection development(BP-GO:0010977), neuron migration(BP-GO:0001764) Nucleic: RNA polymerase II transcription regulatory region sequence-specific DNA binding(MF-GO:0000977), cis-regulatory region sequence-specific DNA binding(MF-GO:0000987), guanyl-nucleotide exchange factor activity(MF-GO:0005085), transcription by RNA polymerase II(BP-GO:0006366), Dbinding transcription activator activity, RNA polymerase II-specific(MF-GO:0001228), Dbinding transcription activator activity(MF-GO:0001216), negative regulation of transcription by RNA polymerase II(BP-GO:0000122), RNA polymerase II cis-regulatory region sequence-specific DNA binding(MF-GO:0000978), transcription regulatory region sequence-specific DNA binding(MF-GO:0000976), Dbinding transcription factor activity(MF-GO:0003700), positive regulation of gene expression(BP-GO:0010628), negative regulation of gene expression(BP-GO:0010629), Dbinding transcription factor activity, RNA polymerase II-specific(MF-GO:0000981), double-stranded DNA binding(MF-GO:0003690), regulatory region nucleic acid binding(MF-GO:0001067), regulation of transcription by RNA polymerase II(BP-GO:0006357), nuclear receptor activity(MF-GO:0004879) Signaling: potassium ion transport(BP-GO:0006813), G protein-coupled receptor activity(MF-GO:0004930), Wnt signaling pathway(BP-GO:0016055), insulin receptor signaling pathway(BP-GO:0008286), transmembrane receptor protein tyrosine kinase signaling pathway(BP-GO:0007169), Wnt signaling pathway(KEGG:4310), steroid hormone receptor activity(MF-GO:0003707), enzyme linked receptor protein signaling pathway(BP-GO:0007167), voltage-gated potassium channel complex(CC-GO:0008076), regulation of smoothened signaling pathway(BP-GO:0008589), ion transport(BP-GO:0006811), solute:cation symporter activity(MF-GO:0015294), ligand-gated ion channel activity(MF-GO:0015276), transmembrane receptor protein tyrosine kinase activity(MF-GO:0004714), organic anion transmembrane transporter activity(MF-GO:0008514), negative regulation of signal transduction(BP-GO:0009968), organic anion transport(BP-GO:0015711), solute:sodium symporter activity(MF-GO:0015370), sodium ion transmembrane transporter activity(MF-GO:0015081), anion transmembrane transporter activity(MF-GO:0008509), anion transport(BP-GO:0006820), potassium channel activity(MF-GO:0005267), potassium ion transmembrane transporter activity(MF-GO:0015079), voltage-gated potassium channel activity(MF-GO:0005249) Metabolic: glycerophospholipid metabolic process(BP-GO:0006650), ATP binding(MF-GO:0005524), phospholipid metabolic process(BP-GO:0006644), negative regulation of biosynthetic process(BP-GO:0009890), negative regulation of macromolecule metabolic process(BP-GO:0010605), positive regulation of metabolic process(BP-GO:0009893), positive regulation of macromolecule biosynthetic process(BP-GO:0010557), positive regulation of macromolecule metabolic process(BP-GO:0010604), negative regulation of metabolic process(BP-GO:0009892), Glycerophospholipid metabolism(KEGG:564), positive regulation of biosynthetic process(BP-GO:0009891), dephosphorylation(BP-GO:0016311), negative regulation of macromolecule biosynthetic process(BP-GO:0010558) Development: determination of left/right symmetry(BP-GO:0007368), animal organ morphogenesis(BP-GO:0009887), lymph vessel development(BP-GO:0001945), determination of bilateral symmetry(BP-GO:0009855), mesoderm development(BP-GO:0007498), gastrulation with mouth forming second(BP-GO:0001702), morphogenesis of embryonic epithelium(BP-GO:0016331), morphogenesis of an epithelium(BP-GO:0002009), specification of symmetry(BP-GO:0009799), embryo development(BP-GO:0009790), vasculature development(BP-GO:0001944), lymphangiogenesis(BP-GO:0001946), tissue development(BP-GO:0009888), microtubule binding(MF-GO:0008017), mesoderm formation(BP-GO:0001707), embryo development ending in birth or egg hatching(BP-GO:0009792), dendrite development(BP-GO:0016358) Sensory: sensory organ development(BP-GO:0007423), eye development(BP-GO:0001654) Stress: chemotaxis(BP-GO:0006935) Circulatory: blood vessel development(BP-GO:0001568), angiogenesis(BP-GO:0001525), integral component of plasma membrane(CC-GO:0005887) Transport: phospholipid transport(BP-GO:0015914), organic acid transmembrane transporter activity(MF-GO:0005342), L-amino acid transmembrane transporter activity(MF-GO:0015179), inorganic molecular entity transmembrane transporter activity(MF-GO:0015318), symporter activity(MF-GO:0015293), transporter activity(MF-GO:0005215), amino acid transmembrane transporter activity(MF-GO:0015171), secondary active transmembrane transporter activity(MF-GO:0015291), lipid transporter activity(MF-GO:0005319), organophosphate ester transport(BP-GO:0015748) Cellular: Focal adhesion(KEGG:4510), protein dephosphorylation(BP-GO:0006470), Cellular senescence(KEGG:4218), regulation of cell morphogenesis involved in differentiation(BP-GO:0010769), cell surface receptor signaling pathway(BP-GO:0007166), cell morphogenesis(BP-GO:0000902), negative regulation of cell development(BP-GO:0010721), movement of cell or subcellular component(BP-GO:0006928), homophilic cell adhesion via plasma membrane adhesion molecules(BP-GO:0007156), protein deacetylation(BP-GO:0006476), cell morphogenesis involved in differentiation(BP-GO:0000904), P-body(CC-GO:0000932), mesenchymal cell development(BP-GO:0014031), cell recognition(BP-GO:0008037), regulation of cell size(BP-GO:0008361), cytoplasmic side of plasma membrane(CC-GO:0009898), cytoskeleton organization(BP-GO:0007010), cell adhesion(BP-GO:0007155), myeloid cell homeostasis(BP-GO:0002262) Catalytic: UDP-glycosyltransferase activity(MF-GO:0008194), transferase activity, transferring acyl groups(MF-GO:0016746), transferase activity, transferring phosphorus-containing groups(MF-GO:0016772), omega peptidase activity(MF-GO:0008242), protein serine/threonine phosphatase activity(MF-GO:0004722), phosphoprotein phosphatase activity(MF-GO:0004721), S-acyltransferase activity(MF-GO:0016417), kinase activity(MF-GO:0016301), palmitoyltransferase activity(MF-GO:0016409), phosphatase activity(MF-GO:0016791), protein tyrosine kinase activity(MF-GO:0004713) Miscellaneous: Ribosome(KEGG:3010), GTPase activator activity(MF-GO:0005096), Regulation of actin cytoskeleton(KEGG:4810), enzyme activator activity(MF-GO:0008047), Adherens junction(KEGG:4520)"	"Prey Capture Probability, Reaction DisNegce (mm), Startle Magnitude Period 2"	"HMM Medium -> Fast TP, Swimming Bout Duration (sec)"