DTSEA User Guide
Yinchun Su, Junwei Han
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
library(magrittr)
library(DTSEA)
#> This package SHOULD NOT BE USED UNDER INTEL MATH KERNEL LIBRARY ON ANY OCCASION.
#> There is an avoidable but critical bug with Intel Math Kernel Library (MKL) on various operating systems.
#>
#> ======================================
#> For better performance, we recommend not using RStudio on Windows because RStudio cannot take advantage of the multi-core capabilities available on modern computers.
Introduction
The Drug Target Set Enrichment Analysis (DTSEA) is a novel tool used
to identify the most effective drug set against a particular disease
based on the Gene Set Enrichment Analysis (GSEA).
The central hypothesis of DTSEA is that the targets of potential
candidates for a specific disease (e.g., COVID-19) ought to be close to
each other, or at least not so far away from the disease. The DTSEA
algorithm determines whether a drug is potent for the chosen disease by
the proximity between drug targets and the disease-related genes. Under
the central hypothesis of DTSEA, the DTSEA consists of two main
parts:
- Evaluate the influence of the specific disease in the PPI network by
the random walk with restart algorithm.
To evaluate the influence, we compute the disease-node distance by
using the random walk with restart (RwR) algorithm, then rank the nodes
reversely.
- Evaluate the drug-disease associations based on GSEA.
The GSEA approach is adopted in this part to identify whether
candidate drug targets are disease-related (top) or disease-unrelated
(bottom) on the human PPI list. The specific disease gene list is
normalized by the median and is set zero as the arbitrary cutoff point
to classify the relations manually.
This vignette illustrates how to use the DTSEA
easily. Here, using functions in this package, users could identify
potential drugs for disease by the DTSEA algorithm.
Example 1: Calculate the enrichment scores of drugs.
The function DTSEA is used to calculate the enrichment
scores of drugs. The parameters are as follows:
network: The human protein-protein interactome network.
It should be or be preconverted before being inputted in DTSEA.disease: The disease-related nodes.drugs: The drug-target long format dataframe. It
includes at least columns with the drug_id and drug_target.rwr.pt: The random walk p0 vector. Set it to zero if
you wish DTSEA automatically compute it, or you can provide your
predetermined p0 vector.sampleSize: The size of a randomly selected gene
collection, where size = pathwaySizeminSize: Minimal set of a drug set to be tested.maxSize: Maximal set of a drug set to be tested.eps: The boundary of calculating the p value.nPermSimple: Number of permutations in the simple fgsea
implementation for preliminary estimation of P-values.gseaParam: GSEA parameter value, all gene-level
statistics are raised to the power of ‘gseaParam’ before calculating
GSEA enrichment scores.verbose: Show the messages.
#> Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.81% of the list).
#> The order of those tied genes will be arbitrary, which may produce unexpected results.
You can arrange the positive results by NES
select(result, -leadingEdge) %>%
arrange(desc(NES)) %>%
filter(NES > 0 & pval < .05) %>% head()
#> # A tibble: 1 × 7
#> drug_id pval padj log2err ES NES size
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int>
#> 1 DB00112 0.00854 0.0541 0.326 0.729 1.82 9
Or we can draw the enrichment plot of the first predicted drug using
fgsea package.
fgsea::plotEnrichment(
pathway = example_drug_target_list %>%
filter(drug_id == slice(result, 1)$drug_id) %>%
pull(gene_target),
stats = random.walk(network = example_ppi,
p0 = calculate_p0(nodes = example_ppi,
disease = example_disease_list)
)
)
Example 2. Get the influence of the specific disease in the PPI
network
The function random.walk calculates the pt
vector. The parameters are as follows:
network The input graph object. It should be either
igraph object or edge list matrix / data frame.p0 The starting vector on time 0.edge_weight Logical to indicate whether the input graph
contains weight information.gamma The restart probability used for RwR. The
gamma takes the value from 0 to 1, controlling the
probability that a node would go back to its starting node.threshold The threshold used for RwR. The
threshold indicates the stabilization status, which is a
stopping criterion of RwR.pt.post.processing The way to scale the pt
vector. It can be ‘none’, ‘zscore’, and ‘log’.pt.align The way to normalize the output
pt vector. It can be ‘mean’ to manually cut the up- and
down-regulated genes, ‘median’ to avoid the influence of the
distribution shape, or ‘none’ for no normalization.
# Calculate p0
p0 <- calculate_p0(nodes = example_ppi, disease = example_disease_list)
# Then perform random walk
random.walk(network = example_ppi, p0 = p0, verbose = FALSE)
#> MYD88 MAPK14 TRAF1 JAK2 AGT
#> 5.010909812 4.994586274 4.985954704 4.970095259 4.964824533
#> IRAK2 C1QB MBL2 JAK1 SERPING1
#> 4.959323416 4.954604290 4.953217930 4.946210760 4.945705136
#> C2 F2 IL1B IL1RAP TOLLIP
#> 4.942325179 4.939415497 4.938276496 4.934206201 4.932806208
#> TLR2 PRKCD C1QBP IL6 STAT4
#> 4.931515441 4.929374468 4.927281284 4.924145466 4.919184876
#> CDKN1A CCR5 CCR2 CCR6 IL2RA
#> 4.918671520 4.918311813 4.914397859 4.914397859 4.911920946
#> PTAFR SOCS1 NFKBIA LTB4R CCND3
#> 4.909615981 4.908947078 4.908900447 4.907826960 4.906926975
#> IRAK3 IL7R GAPDH IRF4 TIGIT
#> 4.906719402 4.904530202 4.904031661 4.902925828 4.901591648
#> TNFRSF9 ABCB1 TNFRSF10C MBP TGFB1
#> 4.901458722 4.900730509 4.899682250 4.899394925 4.898255307
#> ACE BAX CX3CR1 IFITM1 XBP1
#> 4.897801682 4.897102222 4.896630572 4.896167184 4.895007799
#> CD163 B3GAT1 EEF1G FCER1G STING1
#> 4.894973618 4.894102265 4.894086731 4.893819714 4.893241731
#> ICAM3 C8A ATG7 PECAM1 GPR183
#> 4.893088774 4.892732875 4.892471397 4.892383472 4.891961740
#> SKI TAGAP BST2 ADGRE5 FKBP5
#> 4.890495391 4.890110373 4.889783533 4.889770070 4.889415570
#> LILRA6 KLRB1 CCRL2 PTPN6 CCL19
#> 4.889232171 4.888732487 4.888553366 4.166888294 3.791312427
#> MTA1 SRC SYK TRAF2 STAT1
#> 3.694890803 3.354471065 3.218808060 3.188016786 3.137322774
#> CD55 TRAF6 STAT2 IRF3 IRAK1
#> 3.121408749 3.067412335 2.990079526 2.947453222 2.945758279
#> PIK3R1 C5 PRKCA KNG1 C3
#> 2.897909213 2.775559992 2.775339270 2.744454754 2.738667626
#> NECTIN3 PVR NECTIN2 NFKB1 RELA
#> 2.699416510 2.660555027 2.659896088 2.632794743 2.626117131
#> MAPK11 C6 STAT6 VTN JUN
#> 2.614761695 2.590500578 2.572443902 2.560426020 2.556895710
#> C1QA FOS STAT3 IKBKE TRAF3
#> 2.552956290 2.538349970 2.506972026 2.497610424 2.486126768
#> MAPK12 MAPK1 MASP1 TICAM2 TNFRSF4
#> 2.467737087 2.465130252 2.448622312 2.432891982 2.429691929
#> HSP90AA1 PIK3CA CD59 UBC MAPK3
#> 2.426852365 2.418451450 2.417714518 2.415211327 2.414175753
#> MTOR C1QC BDKRB2 IGHV3-23 MAP3K1
#> 2.413117003 2.397067951 2.393377841 2.390425859 2.379130709
#> IKBKB AGTR2 CHUK FYN ZBTB16
#> 2.362008247 2.354242919 2.341270716 2.334839498 2.332458488
#> JAK3 RPS27A HSP90AB1 ESR1 C4A
#> 2.320533347 2.319457270 2.266460741 2.262144811 2.250674414
#> C4B IGHG1 UBB IL1R1 FCN1
#> 2.249931932 2.248996806 2.238058472 2.220522487 2.207140740
#> CD19 NGFR APP ZHX1 CD81
#> 2.201017778 2.192449160 2.176415873 2.126437073 2.123647716
#> CR2 PIK3R2 ABHD16A CAV1 TLR4
#> 2.118684522 2.117479450 2.094738122 2.086543283 2.085256651
#> STAT5A EGFR RAC1 C1R CSNK2B
#> 2.080026898 2.078988468 2.075294800 2.070115224 2.066581303
#> GRK2 AGTR1 LYN MAPK8 TBK1
#> 2.064583103 2.062717655 2.059719100 2.054499222 2.050750133
#> STAT5B PIK3CB PGR CCL23 GNAQ
#> 2.039338034 2.035951951 2.031315458 2.031314117 2.017628633
#> GNB1 PRKCB GNG2 LCK PIK3CD
#> 2.000373553 1.995397473 1.992991465 1.981689006 1.968836350
#> RNF2 CDX2 MAPK10 ANXA1 PLCB2
#> 1.966223059 1.962246143 1.959006170 1.957102313 1.954138942
#> APOA1 PLCB1 HAX1 IL1A SLC22A2
#> 1.954090644 1.951911989 1.937154606 1.918327306 1.915054670
#> SLC22A1 VAV1 RAP1A PIK3R3 CEBPA
#> 1.907237568 1.904245422 1.901758119 1.900143555 1.897242702
#> CXCL8 HBA2 SMAD2 CXCR4 HBA1
#> 1.893480763 1.892265795 1.888878177 1.887353436 1.885541652
#> PRKACA PRKCQ HP PIK3CG HBB
#> 1.885206119 1.882946253 1.875329057 1.869040375 1.866433932
#> CXCL1 ITGB2 RIPK2 MYH9 TYK2
#> 1.855736082 1.855606410 1.852009206 1.847930705 1.847174335
#> CD209 ERN1 ATXN1 FPR2 BDKRB1
#> 1.836819443 1.831616073 1.823427610 1.821589779 1.810625851
#> TNFSF10 IFNA1 MAVS TAB2 LRSAM1
#> 1.803152707 1.780994377 1.779996166 1.772569730 1.772006543
#> AAMP RFLNB GNAI2 SLC27A6 NOS2
#> 1.767224652 1.763118919 1.762323250 1.761888706 1.759830354
#> IFNG MAP2K6 GNAI1 HRAS C5AR1
#> 1.757938593 1.748836792 1.748268844 1.746755155 1.744478821
#> TP53 NFKB2 EZR CALR ARRB2
#> 1.744098541 1.742584979 1.739782510 1.738239787 1.734755790
#> GRB2 SMAD3 AKT1 DDIT3 LOC102723407
#> 1.732660835 1.728394787 1.726973604 1.724090178 1.716653840
#> DCN TNF CXCL13 RELB CASP8
#> 1.711703564 1.710752462 1.705311612 1.702143391 1.701071349
#> GSK3B TBP C3AR1 ITGAL REN
#> 1.700206441 1.697818088 1.697182501 1.695879067 1.695768288
#> MSN BTK PTPN11 MME TNFRSF1A
#> 1.689288008 1.685259120 1.684265840 1.680527359 1.668754771
#> TRIO IL12B EP300 PRKCZ PTK2
#> 1.667251984 1.665910937 1.660227226 1.654188625 1.648799874
#> CREBBP ACE2 ARHGEF12 CXCL10 ITGAD
#> 1.647330136 1.647087940 1.642983354 1.642930455 1.639127439
#> IL2 TIRAP TBPL1 LAT MAP3K7
#> 1.620034602 1.616438226 1.615901592 1.607600236 1.604810176
#> CCL5 NFATC2 ARRB1 CCL20 ARF1
#> 1.599197444 1.594388590 1.586893725 1.569621363 1.566366918
#> CXCL12 GRM1 SDC2 GNA11 THOP1
#> 1.565320678 1.556817952 1.555557388 1.554336978 1.547312209
#> RIPK1 TICAM1 PF4 PPBP CXCR2
#> 1.546766799 1.545794799 1.540143576 1.536445401 1.531919189
#> PDGFRB PRKCG MAP2K3 CCL16 GNA13
#> 1.530971983 1.530819083 1.526885202 1.525078430 1.521913567
#> CTNNB1 CDC42 COMT PLCG2 F12
#> 1.518315877 1.516071879 1.504410387 1.502796237 1.496342163
#> CCL3 GABARAPL2 MAP3K3 CCR1 SOS1
#> 1.480563595 1.476922557 1.474156796 1.460880890 1.458700431
#> TRADD PTK2B CASP3 IKBKG IL12A
#> 1.457629943 1.455000877 1.450347937 1.445536485 1.440108672
#> MAP3K14 SHC1 IRF5 BGN MTNR1A
#> 1.436486864 1.430353694 1.426097151 1.423279415 1.420930852
#> GNA12 GH1 SPI1 HTR2A PLCG1
#> 1.420604397 1.418977035 1.417421834 1.412696667 1.412105072
#> EDN1 MAP1LC3B LRP1 GABARAPL1 HIF1A
#> 1.409288571 1.408566415 1.403741249 1.401020664 1.400988771
#> GABARAP NOD1 ATG12 IFNGR1 MAP1LC3A
#> 1.397748780 1.396908437 1.396297801 1.394905889 1.393146766
#> YWHAB CD14 BCL2 BCL6 ATG16L1
#> 1.384654755 1.384584134 1.383990757 1.376849049 1.376257444
#> IFI16 PRPF40A CCR10 ADRA1B SMAD4
#> 1.374703585 1.373757979 1.371226416 1.366231510 1.363779227
#> GCG CCR3 SKIL TNFRSF1B AKT3
#> 1.363126084 1.362686546 1.362325823 1.360606401 1.353594381
#> CSF2 AVP OXTR ADRA1A CHRM3
#> 1.352481433 1.349865530 1.349826065 1.346628903 1.344823594
#> IFNAR1 FKBP4 PTGER1 SDC4 WIPI2
#> 1.341382578 1.339364445 1.339034006 1.337611657 1.337591755
#> A2M PDGFA ADRA1D P2RY2 CHRM1
#> 1.334816561 1.333750852 1.333744571 1.333706284 1.332247741
#> RHOA GNRH1 TRIM32 CSF2RB CCKAR
#> 1.329443648 1.327787321 1.326753390 1.326404637 1.325260969
#> HSPA8 IRF7 MYOC HTR2B IRS1
#> 1.322829937 1.321768378 1.320215649 1.319809892 1.317598732
#> EGF HRH1 AKT2 PDGFRA TLR3
#> 1.316897553 1.316077521 1.312805303 1.312606136 1.309798411
#> KIT IFNAR2 ADCY6 ADCY3 ADCY8
#> 1.306827072 1.303873297 1.302022359 1.301096940 1.300997373
#> IL12RB1 ADCY1 SDC1 PTPRC ADCY5
#> 1.299845478 1.299143163 1.295151056 1.294945128 1.293923298
#> ITGAV CALM1 PRKACB PRKCI IL10
#> 1.291883126 1.291614355 1.291000726 1.288907372 1.276939759
#> OPRD1 CSF2RA ARHGEF1 ERBB2 FOXO1
#> 1.276704395 1.272962099 1.266580406 1.248436500 1.238788645
#> FOXO3 PLG YWHAG PRKCE KRAS
#> 1.232724033 1.227242969 1.223542281 1.217273599 1.215338601
#> YWHAZ POMC GABBR1 PAK1 HSPG2
#> 1.210635328 1.209714322 1.209178231 1.207388197 1.204586125
#> NRAS EXT2 CALM3 CBL BCL2L1
#> 1.201280096 1.199958232 1.199613226 1.197356742 1.191807555
#> RASGRF2 PML GPC1 INPP5D DRD2
#> 1.188739443 1.187934612 1.177676571 1.177610723 1.176921865
#> OPRM1 MMP2 FPR1 GABBR2 CCL2
#> 1.176556447 1.176256582 1.173880187 1.172895281 1.172866540
#> ACTB FCGR3A CCL7 MTNR1B NPY
#> 1.170888617 1.163216357 1.156830432 1.154956091 1.154501533
#> OPRK1 ADORA2B S1PR1 SETDB1 ADORA2A
#> 1.149070049 1.146691160 1.144318985 1.144203297 1.143666500
#> HTR1A CSNK2A1 ADRA2C ELANE CCL11
#> 1.140182579 1.139623597 1.138563849 1.136884270 1.136549610
#> ADORA1 SDC3 KITLG VCAN HRH4
#> 1.135904354 1.129784280 1.129404596 1.128871931 1.127339601
#> APLN CCL18 GNAT3 NCOR1 PLAT
#> 1.125217590 1.124978873 1.124520458 1.122578040 1.120418193
#> PIAS4 ACKR3 CSPG4 GRK1 ABL1
#> 1.118813370 1.117636729 1.116170929 1.114718654 1.113977465
#> GPC4 YWHAE GPC3 SELP CRP
#> 1.109462808 1.101944790 1.100057235 1.099974392 1.098091607
#> SELE RBX1 BIRC2 GADD45A DYNLL1
#> 1.097191412 1.093467101 1.087121905 1.081303102 1.077465028
#> BCAN CSF3 ATN1 SMAD1 SP1
#> 1.075777972 1.075736764 1.074536149 1.073341729 1.068956564
#> MALT1 NCAN SIN3A TLR9 CAMK2B
#> 1.066189317 1.065299291 1.062986888 1.058662981 1.056244764
#> EIF2AK2 CD93 GLI3 VDR CCND1
#> 1.050503348 1.038305065 1.037100488 1.035417535 1.028736249
#> EPOR ACTG1 GLI2 EEF1A1 CNTF
#> 1.015319176 1.010158790 1.007414778 1.006222656 1.004870793
#> IL11 CD36 TEK PIAS1 TLR7
#> 1.004021872 1.003075148 0.990580760 0.988133976 0.984894163
#> ITGB3 PCNA SNW1 SPOP TOM1L1
#> 0.979987981 0.978731996 0.977077695 0.969921388 0.967743692
#> IL21 SMAD9 CSF3R NOD2 DAZAP2
#> 0.965973868 0.965712233 0.961345879 0.958355890 0.956613130
#> LEP CD46 KRT1 MAD2L1 KIR2DL4
#> 0.953128620 0.947984654 0.947736310 0.942652611 0.937668556
#> HIPK2 DEFA1 CEBPB RAC3 MAP3K5
#> 0.937041661 0.930558535 0.929925036 0.916285816 0.915548905
#> THBS1 MAPK6 RBPMS HTT RPS3
#> 0.910301802 0.907881576 0.905230883 0.902546681 0.900628993
#> TIAM1 CALCR MYC GP6 B4GALT3
#> 0.899307578 0.899010486 0.897588569 0.893459712 0.891812882
#> C4BPA SPTAN1 TOM1 B4GALT1 GNA15
#> 0.889067721 0.884220554 0.878539928 0.876217278 0.875514707
#> IL15RA LDB1 GP1BA BID XRCC6
#> 0.875214582 0.866863997 0.865633201 0.863609217 0.861769707
#> FADD MAP2K4 CDK4 RACK1 TGFBR1
#> 0.859034855 0.852882008 0.851204785 0.845531223 0.842945498
#> HLA-DRA SEPTIN1 LEPR BRAF MAPKAPK5
#> 0.841180915 0.840141270 0.834596626 0.822227483 0.818307899
#> CSK PSMA4 NCR1 PDPK1 ADRB2
#> 0.816698787 0.810998322 0.806046230 0.805090015 0.803015807
#> SOCS6 SOCS7 GP1BB PARD3 ESR2
#> 0.798866194 0.791967965 0.790820341 0.785364712 0.783911127
#> TUBB FGFR3 IL18R1 IRF9 CAMK2A
#> 0.783766289 0.783647395 0.782572202 0.780801401 0.779326125
#> PTPN1 RAF1 RHOB CUL1 FGFR2
#> 0.775554673 0.771454698 0.770725676 0.766562550 0.764577368
#> ERBB3 RIPK3 IL36RN HDAC1 KAT5
#> 0.764324153 0.763677755 0.755888436 0.755144447 0.752808169
#> PPP2CA GRIN1 CDKN1B RHOG GAB2
#> 0.750645329 0.747078748 0.747004960 0.743936318 0.737042480
#> CAMK2D PRMT1 AR ITGA5 DEFB103A
#> 0.736589443 0.726017439 0.721074408 0.719920271 0.718288342
#> HCK SLC25A5 F11 RASGRP3 CAPN1
#> 0.712007246 0.705187333 0.702518047 0.689140151 0.686349939
#> GNB2 DLG4 FGFR1 MMP14 NEFL
#> 0.683639195 0.681896830 0.677372627 0.674939702 0.670337230
#> GRIN2B CISH ABR PIM1 DSP
#> 0.665612314 0.661176699 0.658887933 0.657805143 0.657473558
#> CDC25A FGF1 FGF7 RHOQ RHOH
#> 0.657167232 0.656528148 0.656118863 0.654231616 0.652644875
#> PPP1CA YWHAQ MAG CASP1 GNB5
#> 0.652431768 0.651617234 0.650002883 0.649517706 0.648892928
#> SMURF2 MMP7 RAN H4-16 ARHGEF7
#> 0.644619494 0.644261981 0.643999032 0.637755225 0.637078206
#> FRS2 CD40 FGF10 SQSTM1 GRIN2D
#> 0.634290547 0.633516377 0.624675717 0.620869691 0.611106198
#> ITSN1 JUP TK1 EFNB2 SUMO4
#> 0.608989870 0.608364586 0.606628593 0.596483108 0.596475089
#> ARHGDIA PLP1 ARHGEF6 MAP3K8 GRIN2A
#> 0.596277596 0.595136816 0.593509671 0.588400955 0.586102090
#> NCK1 ACTN2 ARHGEF18 RASGRP1 NGEF
#> 0.583871139 0.581675708 0.577097416 0.575742051 0.572513471
#> SH3GLB1 NEK9 CD4 GAB1 USP7
#> 0.566727614 0.561769529 0.561045842 0.559977782 0.559068628
#> ANGPT1 HES1 AKAP13 KL ELK1
#> 0.558680579 0.557174441 0.554389924 0.553953064 0.550167943
#> STAP2 ARHGEF2 ARHGDIB HABP4 TGFBR2
#> 0.549857449 0.549638105 0.546776174 0.546399629 0.544632669
#> MED31 AXL SUMO3 COL2A1 CD38
#> 0.544378643 0.542420563 0.541033560 0.540539457 0.537479276
#> ARHGEF11 TIAM2 CREB1 ARNT RASGRF1
#> 0.535553362 0.530706818 0.529686227 0.529644775 0.529204924
#> CHD3 NFATC1 TLK1 KDR ECT2
#> 0.523859760 0.521780379 0.520704519 0.513667056 0.511219912
#> FLT3 UBE2D1 FGD4 NAP1L1 NCAM1
#> 0.506567550 0.500609036 0.499410917 0.499028412 0.498777629
#> CASP10 BTC UBE2I DAXX FGB
#> 0.497253241 0.495632641 0.493017692 0.489660468 0.489308050
#> CASP9 BCL10 FRS3 CDKN2A NFE2L2
#> 0.485122532 0.481593517 0.477258859 0.476977967 0.476794278
#> ITGB6 CSNK2A2 SMURF1 PYCARD BRCA1
#> 0.471857488 0.470212035 0.468233120 0.464734423 0.461746945
#> GNAO1 HSPA1A GNG12 CDK14 TNFRSF11A
#> 0.454912050 0.454547696 0.451433285 0.445622990 0.444483538
#> VDAC1 HMGB1 CASP4 GNG11 COMMD1
#> 0.444143479 0.438364738 0.434090575 0.433904785 0.431609169
#> CCT7 FN1 NGF U2AF1 YAP1
#> 0.431304105 0.430448954 0.430119862 0.427086963 0.425996499
#> GFAP NCOA2 ATF2 CRK HSF1
#> 0.425634464 0.423415068 0.422308573 0.419981826 0.419165062
#> RPL13 ITK RUNX1 BTRC PPP2R1A
#> 0.413202825 0.401461654 0.396355352 0.395353315 0.395141825
#> NUDT21 AOX1 FHL1 HSP90B1 NCK2
#> 0.394331598 0.392362068 0.388358161 0.385722182 0.383327213
#> PRNP ATF4 SIRT1 SUMO1 SFN
#> 0.382409214 0.376548944 0.375366746 0.374628061 0.369986198
#> SAT1 GNB3 RPS27 CCNH GNGT1
#> 0.369277821 0.368320496 0.368238140 0.366609857 0.365090554
#> CD226 EIF3I AREG GNG7 BMP2
#> 0.364898164 0.363564991 0.361087488 0.354540809 0.353057082
#> CYCS PLA2G4A COIL ANXA7 CARD9
#> 0.342962528 0.339134131 0.335250401 0.334010622 0.333448626
#> GABRB1 FLNA BCR SH3GL2 BCL3
#> 0.331344735 0.329576786 0.324281226 0.320076826 0.319741622
#> PRKN EPAS1 MAP2K1 CDK1 RPLP1
#> 0.319189225 0.313584012 0.311317855 0.305080568 0.304912769
#> HDAC5 APAF1 HSPA4 SRSF1 CRKL
#> 0.300963320 0.300545348 0.299995482 0.296566928 0.294469053
#> FCGR1A CCN2 CYP27B1 PRRC2A ITGA2B
#> 0.291547617 0.289372810 0.288000434 0.287645252 0.286380722
#> TRIB3 CSF1R CD247 EFEMP2 FLII
#> 0.285664748 0.285203770 0.285015872 0.280938909 0.279818701
#> MET SNCA DDX5 NONO SFPQ
#> 0.279043648 0.275670041 0.272910326 0.269334523 0.267315394
#> CASP2 TRIP6 ENG DDX3X CASP6
#> 0.267178423 0.261273999 0.259862812 0.257879581 0.253886555
#> MAPK4 FNTA RPS6 IGF1 PPP2R1B
#> 0.253046844 0.252815989 0.251950587 0.248672482 0.247895669
#> GFI1B LTBP1 EFNA1 NCF1 OLR1
#> 0.244632159 0.234788706 0.233750632 0.228884086 0.228091527
#> SERPINE1 AFDN FGA HRK SFTPA1
#> 0.227896696 0.227228023 0.219429443 0.219366695 0.218174632
#> CDKN2B RPS10 CDK2 NDRG1 HNRNPA1
#> 0.215342846 0.214687826 0.212289192 0.210684377 0.210157781
#> EXOSC6 CREB3L3 MAP3K2 ACVRL1 AIFM1
#> 0.209196030 0.209060228 0.208549111 0.208342616 0.204486205
#> CTNNA1 EIF3K HSPD1 DTNBP1 ATP5F1C
#> 0.202088097 0.199257943 0.197999330 0.191957056 0.191938346
#> GZMB PTHLH ITGB1 CR1 TNNT1
#> 0.188738744 0.188316935 0.188041242 0.182588128 0.182324671
#> FCGR2A NCOR2 SLC2A1 ANP32A NUP85
#> 0.178147421 0.174371592 0.172195463 0.164973895 0.164728067
#> CDKN1C RPL7A F5 CDK11B CLTC
#> 0.164294886 0.164006479 0.162490352 0.160355642 0.151204979
#> HK2 HK1 TOMM20 INS ITGAM
#> 0.148086906 0.147414658 0.144702035 0.140902279 0.137189855
#> AKAP8 IGFBP3 DEFB4A CSF1 RPS6KA1
#> 0.130931948 0.129925802 0.127477391 0.115641485 0.108931118
#> HDAC3 AP1M2 CAMK4 ATF5 CSTF2
#> 0.108749445 0.108058105 0.105029412 0.095010377 0.089801051
#> LAMA4 RASA1 DNM2 CUL5 BCAR1
#> 0.089798120 0.088816828 0.081616830 0.076955744 0.076819714
#> AGER EEF1B2 VEGFA NCOA3 CDK5RAP2
#> 0.075648487 0.068533597 0.066399335 0.063867939 0.056452434
#> CTSG ARL15 HMOX2 FBXW11 DRD3
#> 0.056238112 0.048743459 0.047228900 0.045528824 0.044867734
#> CYBB DYNC1I1 NCF2 PPP2R2A SNAPIN
#> 0.044082544 0.034521138 0.031394000 0.019028769 0.010418640
#> LAMTOR5 CCNB1 CYBA ITGB3BP POM121
#> 0.001284915 -0.001284915 -0.002032472 -0.002257284 -0.004108970
#> GSTO1 CTSZ ACVR1 NR3C1 RXRA
#> -0.004198547 -0.008430929 -0.008476105 -0.018392323 -0.021727082
#> HLA-A CCDC106 FES ARR3 TSHR
#> -0.023366473 -0.024109960 -0.024968344 -0.026065210 -0.027458073
#> COPS6 PTEN H3C14 PTGS2 NADK
#> -0.028370834 -0.030734784 -0.049197975 -0.054029047 -0.057012938
#> BTBD2 ACTC1 ERCC6 DDX58 C11orf58
#> -0.060562890 -0.063194598 -0.063636227 -0.066006987 -0.066993203
#> H3C1 BMPR1B CHFR EPRS1 GSK3A
#> -0.076637869 -0.079510253 -0.079824379 -0.105699407 -0.107472962
#> COL4A5 CTSB CAMK1 H3-3A PPARA
#> -0.109602029 -0.112359720 -0.115352485 -0.127187638 -0.143708928
#> BMPR2 PXN MED1 HSPA5 ALK
#> -0.147221700 -0.147961123 -0.161381304 -0.162610191 -0.163903596
#> ITGB4 PAK2 TTF1 PLD1 GOT2
#> -0.166546705 -0.172922226 -0.174326165 -0.184092117 -0.184247795
#> FGF2 CCNB2 F2RL1 MDK HNRNPU
#> -0.185554414 -0.188606428 -0.196334300 -0.196518371 -0.199429939
#> LRIF1 OSTF1 XPO1 MAPT DCTN1
#> -0.200064164 -0.205359916 -0.221789743 -0.229883345 -0.232388653
#> FURIN MAP3K4 EWSR1 ARAF ABI1
#> -0.233597994 -0.234396308 -0.237089388 -0.237407563 -0.238401710
#> CD9 UBE2N COPS2 XIAP BLOC1S1
#> -0.240855461 -0.242223915 -0.243270869 -0.248384265 -0.254059369
#> FCGR2B CDC37 ANGPT2 THBD CARM1
#> -0.266836954 -0.268748729 -0.269471652 -0.276848143 -0.277287615
#> ATP5F1B MAPKAPK2 AMBP SIVA1 ST13
#> -0.286920748 -0.292610448 -0.311001389 -0.316548556 -0.330106297
#> NCOA1 FAF1 MAPK7 COL1A2 USO1
#> -0.332056337 -0.333522720 -0.337550833 -0.343744894 -0.346772167
#> CYLD PPARGC1A PEBP1 APOE DCTN2
#> -0.347644645 -0.350716518 -0.353232110 -0.353696669 -0.355469942
#> CTLA4 COL1A1 DVL2 CCNA2 PICK1
#> -0.356059258 -0.358789497 -0.370889722 -0.372949847 -0.381884803
#> RRAS MLST8 ATXN3 PSMA3 ITGA2
#> -0.384422171 -0.389876616 -0.397707140 -0.400017299 -0.401745286
#> PPM1A TUBA4A AANAT NOTCH1 TMEM62
#> -0.412467394 -0.413895117 -0.416632626 -0.417120565 -0.417534940
#> RXRG ACTA1 HLA-DPA1 PKM CDC25C
#> -0.418543625 -0.421738334 -0.422218807 -0.422577119 -0.427903388
#> ITPR1 CADM1 UBQLN4 NTRK1 PILRB
#> -0.429786771 -0.431359865 -0.432033810 -0.433382158 -0.440239820
#> JMJD7-PLA2G4B PASK ITGB5 KRT18 COPB1
#> -0.441653826 -0.444698043 -0.446242262 -0.446833843 -0.450696433
#> WAS NDUFA6 CTSD MAOA RET
#> -0.452734397 -0.453985431 -0.460033038 -0.460825667 -0.471820262
#> KHDRBS1 CCNE1 RGS2 ACTA2 CCDC85B
#> -0.478558888 -0.478744862 -0.481758733 -0.483132459 -0.485476506
#> GABRA1 CD44 DNAJA3 PLK1 HADHB
#> -0.486892670 -0.492978433 -0.494236543 -0.494385812 -0.496100881
#> MED19 RORA NOS1 CDC25B FOLR1
#> -0.499767362 -0.512849048 -0.515993107 -0.517098097 -0.517986026
#> DLG1 LIMK1 MDM2 BAIAP2 UPF1
#> -0.518624941 -0.519642146 -0.521609763 -0.522341011 -0.522625399
#> OCRL MDFI CRELD2 PRKG1 COPA
#> -0.523390116 -0.524351207 -0.527376970 -0.531092781 -0.532943724
#> GNAS SPAG9 MMP9 DUSP3 COPG1
#> -0.533753794 -0.539921477 -0.543135974 -0.544278916 -0.545586524
#> CHEK1 BLNK SCMH1 INPP5B DAB2
#> -0.545917362 -0.549104263 -0.552636835 -0.552909325 -0.558100744
#> ATF1 CD274 COL4A2 RPS6KA3 AURKB
#> -0.566088972 -0.574789740 -0.577606026 -0.584318627 -0.584710797
#> PTN KAT2B ACTN1 UBE3A GRB10
#> -0.586053592 -0.589612918 -0.589860733 -0.590901170 -0.593685873
#> COPS5 PRKAB1 EEF1A2 CAMK2G NSF
#> -0.594025509 -0.596235844 -0.600015150 -0.600828949 -0.601805141
#> FCGR2C H2AX PLA2G6 GDF9 CDH2
#> -0.606117070 -0.608613890 -0.609609942 -0.621221374 -0.623839860
#> NUP153 CBLB PSEN1 FLT1 ADD1
#> -0.624035598 -0.624573848 -0.627101226 -0.632036474 -0.635402528
#> ATP5MF BAD MYL2 CYTH1 DOK1
#> -0.635739796 -0.638485825 -0.644312462 -0.647515075 -0.651191651
#> NFATC4 APCS ACTN4 PPP2R5C ARPC3
#> -0.656314270 -0.663144273 -0.672081700 -0.677788277 -0.679437711
#> EIF3F AP2B1 ADRA2A PAK3 RPS6KA6
#> -0.679764464 -0.682973867 -0.689265351 -0.692870036 -0.699009616
#> PRKAA1 ATP5MC3 TRIP10 TMSB4X ARHGAP15
#> -0.701750235 -0.702503940 -0.706089533 -0.707744696 -0.707987702
#> NUP62 AFAP1 CDH1 APOA2 CSNK1D
#> -0.711787600 -0.712171611 -0.712334720 -0.713436414 -0.715168879
#> SYT1 AP2M1 YWHAH ARHGAP5 ITCH
#> -0.716511443 -0.716964982 -0.717354294 -0.739780929 -0.741717416
#> ETS1 UBQLN1 MYL12A CTTN LRP2
#> -0.744700641 -0.745320105 -0.746163189 -0.748724586 -0.749537890
#> CAD CETN2 GRIA1 CTNND1 LHCGR
#> -0.754116110 -0.754926295 -0.755204921 -0.757781262 -0.758138671
#> HNF1A KLF5 TEX11 FGR EPHB2
#> -0.760857786 -0.760865428 -0.763673035 -0.768617197 -0.769655023
#> PRG2 PFKL ELMO1 L1CAM CTSL
#> -0.772693174 -0.783140938 -0.785472863 -0.786034112 -0.786390006
#> KHSRP ADAM9 DUSP4 PAK6 LPL
#> -0.795467155 -0.797463571 -0.800603660 -0.803107333 -0.804391186
#> CD3D ESRRA LSP1 PPIF CANX
#> -0.804634883 -0.804890793 -0.813986674 -0.817781737 -0.822137502
#> AP2A1 CHRNA7 PPP1CC PTPN12 NR4A1
#> -0.822468776 -0.828182001 -0.835054553 -0.835751505 -0.838631097
#> ADM H3-4 CD28 CRMP1 AXIN1
#> -0.841058636 -0.842903607 -0.847885408 -0.848008933 -0.848736600
#> SLC9A3R1 PPARG THRB EPHA2 ARHGAP10
#> -0.849079134 -0.850043548 -0.851656642 -0.856910273 -0.858595939
#> CHN1 ORM1 TPR CASP7 CD80
#> -0.861567296 -0.864414253 -0.868770220 -0.870408303 -0.876277636
#> MARCKS SVIL CSNK1A1 B2M CACNA1D
#> -0.876288938 -0.881303511 -0.893209268 -0.893245213 -0.895202873
#> NTRK2 CHRNA4 BARD1 CACNA1C TRPC6
#> -0.895395628 -0.896356533 -0.900023883 -0.915378320 -0.935029879
#> ILK PKN1 GABPB1 ADCYAP1 BMX
#> -0.944639986 -0.950036932 -0.957165838 -0.959924013 -0.960185524
#> CYP1A1 TRIM24 NTRK3 AP1M1 PIP5K1C
#> -0.961213087 -0.962372787 -0.963394055 -0.963549222 -0.964980159
#> PPP1CB CEP43 HCLS1 F11R PFDN1
#> -0.967076629 -0.968874468 -0.975089817 -0.982974267 -0.986781396
#> ITGA7 ANXA6 SEC13 GRB7 CD5
#> -0.989857103 -0.990043254 -0.990285108 -0.992364933 -0.992736718
#> BAG6 CD47 ACVR2A RPA1 ANXA2
#> -0.997924807 -0.999365245 -1.000575626 -1.007506675 -1.008258353
#> CSNK1E NRIP1 EPHB1 ATM FLT4
#> -1.012182048 -1.018032208 -1.020964852 -1.021466334 -1.023773107
#> CACNA1S CDH5 POU2F1 STXBP1 EIF2AK4
#> -1.035459900 -1.036517485 -1.039351932 -1.041068290 -1.046795585
#> ERG28 UGT1A1 CACNA1F COL3A1 STX1A
#> -1.047677911 -1.052566995 -1.059897646 -1.062427250 -1.071315665
#> ITGA1 EFNA5 CHRNA3 CHRNB4 PPFIA1
#> -1.072439670 -1.075345357 -1.076427261 -1.076427261 -1.076612737
#> CDK5 BECN1 DLST CTSK ADCYAP1R1
#> -1.076725077 -1.097071011 -1.100735030 -1.103143567 -1.103984497
#> FLNC SMARCA4 ANAPC5 ARF6 TTR
#> -1.107141215 -1.116265452 -1.119225142 -1.127946159 -1.129032499
#> DDB1 TH PIK3C3 CTSS ACP5
#> -1.131968271 -1.134947400 -1.138994084 -1.141086749 -1.143251580
#> PSMC5 PSMC2 EFNB1 CUL3 PLK3
#> -1.143617559 -1.151067464 -1.159164734 -1.160556569 -1.160857655
#> SREBF1 CEBPG PTGES3 PTGER2 MYLK
#> -1.160973864 -1.172173788 -1.174413911 -1.184837538 -1.189826613
#> CEP70 EIF4B HIPK3 CTSC AMPH
#> -1.192558968 -1.193745140 -1.204453571 -1.207152719 -1.208270723
#> RB1CC1 DRD1 CUX1 NUP214 PDE6D
#> -1.214422530 -1.219415965 -1.224293003 -1.228727821 -1.228754309
#> IQGAP1 RIMS1 LMNA CYTH2 NUP98
#> -1.230239214 -1.237400820 -1.243827165 -1.245521195 -1.249197946
#> SMC1A PRKAR2A AHR APBB1IP DRD5
#> -1.258105672 -1.260649122 -1.276340379 -1.281103004 -1.281409462
#> CPLX1 BATF3 HTR7 PRKAR1A KLF2
#> -1.285660407 -1.293844517 -1.295197757 -1.301066928 -1.303199978
#> CENPJ CDC27 NUP160 COL7A1 FXR2
#> -1.303542662 -1.305862403 -1.306330506 -1.314263160 -1.315977878
#> HTR6 ATF7IP APOB FZD4 ATP1A1
#> -1.317788307 -1.319096003 -1.319131616 -1.320635505 -1.321399787
#> CAV3 EPHA3 NUP107 CHRNA9 PPP3CA
#> -1.323879058 -1.324094186 -1.324426174 -1.325654501 -1.343953367
#> CAV2 ATP5F1A PAFAH1B1 APC OCLN
#> -1.346293583 -1.348973780 -1.354841957 -1.355435056 -1.360767902
#> DGKZ BDNF BUB1B GPRASP1 CLASP1
#> -1.361051058 -1.366089294 -1.369295767 -1.369335749 -1.381893617
#> CEP126 CUL4B KLK2 ZNF746 ACAT2
#> -1.383497400 -1.390021442 -1.396683512 -1.396684858 -1.413130380
#> FKBP1A NPPA ASAP1 BIN1 BCAS2
#> -1.413323279 -1.414790487 -1.419850870 -1.426957013 -1.431545381
#> FZD3 TFRC FKBP2 EPN1 NEDD4L
#> -1.438444140 -1.441544381 -1.442822436 -1.451002004 -1.451393166
#> MYLK2 TOP2A ATG101 GPR45 PLA2G2A
#> -1.454112367 -1.459376139 -1.461181201 -1.462619702 -1.466658916
#> MAD1L1 ANAPC10 LUC7L2 DPP4 ALB
#> -1.472822902 -1.474620307 -1.481171021 -1.482636146 -1.483405377
#> NRP1 BIRC5 ULK2 ADRB1 WNT1
#> -1.483882832 -1.487034495 -1.489727070 -1.489965117 -1.499080321
#> GJA1 ERCC8 B9D2 SGK1 PDIA3
#> -1.501169243 -1.512787101 -1.518939148 -1.519194618 -1.525399247
#> NR3C2 HNRNPA0 IMMT ASH2L ENTPD1
#> -1.525801313 -1.530498705 -1.530505388 -1.530809335 -1.538513960
#> FBF1 PINK1 COL18A1 NUP54 GCK
#> -1.552417229 -1.554790347 -1.556371836 -1.560875348 -1.561691598
#> LDLR PDE6G PNP AKR1C3 AKT1S1
#> -1.571111098 -1.575550862 -1.581497664 -1.583332630 -1.584883247
#> PAK4 CCAR2 NDUFA13 HLA-DMB CACNA1A
#> -1.585050857 -1.587645277 -1.587833616 -1.589115738 -1.590253868
#> NDC80 BAG4 EPHA8 ENPP1 CDC73
#> -1.596218503 -1.596333332 -1.596395140 -1.598662101 -1.600802882
#> APBB1 CST3 CACNB4 CD74 CFL1
#> -1.602017271 -1.610187994 -1.612006052 -1.612590144 -1.613307080
#> MARK4 FZD5 HADHA KPNA2 ABCA1
#> -1.614906987 -1.617675255 -1.626074872 -1.626102953 -1.626351705
#> RAB8A CACNA1B APOBEC3C AAAS APEX2
#> -1.628371463 -1.628471881 -1.630496323 -1.632440381 -1.634078399
#> GNAL PI4K2B NR5A1 FGF21 HMGN1
#> -1.638425647 -1.639098719 -1.646890029 -1.653288969 -1.656295778
#> CACNB1 BMP4 HNRNPR EIF2B1 PIK3C2B
#> -1.662940407 -1.663718231 -1.677714799 -1.686205971 -1.687167395
#> AHSP CACNG2 CDIPT BUB3 CDK11A
#> -1.689168516 -1.691050199 -1.692108863 -1.694355653 -1.694669288
#> CACNG4 EPB41 GIPC1 FASN SOD1
#> -1.704973996 -1.707130282 -1.707296845 -1.708748787 -1.709272088
#> WEE1 ASAP2 SHBG PIK3C2A TAOK1
#> -1.715712657 -1.719461776 -1.720807102 -1.721455872 -1.725544216
#> ABCB11 DDOST INPP5E CACNB3 PLA2G1B
#> -1.725905751 -1.737054142 -1.742107109 -1.742570035 -1.744007835
#> GSTP1 ASCC2 NDUFS6 PMF1 MAGEA11
#> -1.745805937 -1.745981024 -1.758056807 -1.763848224 -1.776038535
#> MTMR4 FZD2 ADAP1 AP1B1 CTBP1
#> -1.777402122 -1.777612853 -1.777636394 -1.782478137 -1.795014600
#> DAPK1 ANAPC1 KCNJ6 RBBP5 PDE9A
#> -1.798006177 -1.798116767 -1.799160197 -1.801804824 -1.804883644
#> TIMP1 BST1 NDUFB11 RAD23A AKAP5
#> -1.809494063 -1.823552362 -1.825490794 -1.830109890 -1.836784708
#> GPRASP2 ATR ADAM17 BMP1 PDE1A
#> -1.838358654 -1.851213737 -1.851904893 -1.852388624 -1.865358908
#> FABP4 CFTR CHEK2 NDUFB10 APEH
#> -1.866028341 -1.869688640 -1.871240655 -1.872445482 -1.875001556
#> MPDZ ADAM10 ECSIT AATF CACNG3
#> -1.877909631 -1.879426858 -1.888239822 -1.888863550 -1.889899987
#> ABI2 RYR2 APPL1 CASR RHEB
#> -1.891357815 -1.897536302 -1.902483915 -1.903401954 -1.904864748
#> DUSP6 BAG1 KCNJ3 PPP2R5D PDE3B
#> -1.910262023 -1.917174129 -1.947050719 -1.947259587 -1.950626505
#> MAP1A MYL10 LGMN KCNJ5 SGK3
#> -1.955096170 -1.959250770 -1.964983776 -1.981597775 -1.983669780
#> CACNB2 DRD4 BUB1 PTGDS CRTC2
#> -1.986082311 -1.990681566 -1.990787878 -1.992777455 -2.001598383
#> NDUFA7 CACNA2D2 CYP2B6 NDUFV3 CYP3A4
#> -2.003233030 -2.010937438 -2.015915425 -2.025508176 -2.027901121
#> CACNA2D1 CACNA2D3 CACNA2D4 NR0B1 CPT1A
#> -2.031091848 -2.031091848 -2.031091848 -2.032505069 -2.042789097
#> CACNG1 CACNG5 CACNG6 CACNG7 EDF1
#> -2.061386208 -2.061386208 -2.061386208 -2.061386208 -2.075014736
#> LGALS3 POLR2M CD24 AKAP12 HTR2C
#> -2.083237452 -2.083376659 -2.088189899 -2.088508636 -2.089157100
#> PTK6 NEDD8 DDR1 DLG3 SLC9A3R2
#> -2.095685858 -2.099940044 -2.101303401 -2.108602873 -2.116265836
#> BUB1B-PAK6 PDE4D RCAN1 AMBRA1 AGAP2
#> -2.117153779 -2.119937794 -2.120443976 -2.122276562 -2.122299769
#> TRPC1 NEK6 SYMPK ACP1 RGS12
#> -2.129794913 -2.131947488 -2.133674353 -2.134970174 -2.140826386
#> RGS19 PDE4A DES DAP3 RAB13
#> -2.153250557 -2.158347753 -2.171777194 -2.172736428 -2.173891553
#> POU1F1 UCP1 SYNGAP1 CACNG8 ARFGEF2
#> -2.179519738 -2.180662383 -2.187337399 -2.189292768 -2.189786385
#> TUBB1 ATP5PF NUDC BACE1 PDK1
#> -2.193264551 -2.197433831 -2.207354433 -2.212808874 -2.213735811
#> FANCG TGFBRAP1 NSMAF KIDINS220 POLA2
#> -2.221545700 -2.223955399 -2.223969888 -2.233442705 -2.236308833
#> PLAAT3 PDE10A PDE3A CYP1A2 A1CF
#> -2.238344852 -2.241643192 -2.244747125 -2.246514194 -2.248535828
#> GC MEFV MIR143 PDE6A PDE6B
#> -2.257221864 -2.274129786 -2.276868660 -2.279370917 -2.279370917
#> AMOT ADRM1 GUCY1B1 DHFR ACACA
#> -2.291838028 -2.294730137 -2.301309337 -2.302678951 -2.312972687
#> PDE1B AIMP2 CACNA1G CACNA1H UQCRQ
#> -2.313059380 -2.314472456 -2.322483157 -2.324045696 -2.324321019
#> PDE4B DDX54 MAP2K5 DCK PDE4C
#> -2.351466879 -2.357511776 -2.359802987 -2.370840048 -2.377436453
#> BLK APBA2 AIP EPB41L1 CYC1
#> -2.381497792 -2.386592220 -2.388946544 -2.401164813 -2.401366305
#> CAPZA1 STK3 CYP17A1 PITPNB PDE1C
#> -2.406468406 -2.408037988 -2.410740435 -2.412966003 -2.416341579
#> GUCY1A2 CHD9 PBX1 CRYAB ARHGEF28
#> -2.428259749 -2.430629720 -2.435985893 -2.452832491 -2.455387802
#> NR4A2 FCHO1 CACNA1I CYP2E1 SCNN1A
#> -2.459363418 -2.462299074 -2.464175929 -2.465938800 -2.473679876
#> AKAP6 MYLK3 MYLK4 NR1I2 MPP1
#> -2.480205521 -2.482311980 -2.482311980 -2.484480638 -2.485952374
#> DPM1 ENTPD6 APLP2 VSNL1 NCAPH
#> -2.489517692 -2.489921323 -2.493077339 -2.495755145 -2.500900799
#> CACNA1E CCNT2 LRAT AMOTL2 AKAP9
#> -2.510517824 -2.523169843 -2.523822834 -2.534605046 -2.547633959
#> ALOX5 AP4M1 SDHA GAK C8orf33
#> -2.549282694 -2.553060008 -2.572215411 -2.577850068 -2.580563634
#> GUCY1A1 AMH MYL3 ECHS1 NAMPT
#> -2.580993670 -2.584401491 -2.592548650 -2.600982239 -2.603381263
#> PDLIM5 NUCB1 MPP3 ARHGAP21 ACADM
#> -2.608868127 -2.619856975 -2.619906016 -2.623683474 -2.658254475
#> AK9 KCNAB2 PDE5A CAMKK2 NPR1
#> -2.664016887 -2.676560833 -2.681024762 -2.698379786 -2.698987227
#> COMMD8 DCAF6 EXOSC1 NNT CIB1
#> -2.701261263 -2.716147051 -2.737886193 -2.738335335 -2.741530069
#> KCNH2 CAMKK1 ABCC8 AHNAK ADA
#> -2.743658753 -2.750851289 -2.782620022 -2.784708256 -2.788214764
#> EPB41L2 AKAP1 NT5E CYP11B1 DUT
#> -2.788939469 -2.800256399 -2.802633607 -2.802927163 -2.803288628
#> DYNLT1 ALOX12 CHRNA1 ALOX15 ADSS2
#> -2.805564459 -2.806561877 -2.811961967 -2.858629227 -2.860470662
#> PDE6H PTGS1 AKR1C1 GUCY2C ANKS1B
#> -2.864836662 -2.869279217 -2.871538080 -2.889266093 -2.909769680
#> ROBO2 PDE2A ALDH2 NT5C2 BICD2
#> -2.910547484 -2.915865198 -2.942765494 -2.948748248 -2.956473522
#> PDE6C CLSTN1 HSD17B6 APPBP2 WDR61
#> -2.967534324 -2.988715839 -3.019379999 -3.035437367 -3.042129539
#> PDE7A PDE7B PDE8A PDE8B ARL2
#> -3.056685449 -3.056685449 -3.056685449 -3.056685449 -3.057196872
#> CHRND KCNA2 LTA4H NT5C CYP11B2
#> -3.070092326 -3.071158528 -3.096071509 -3.099086074 -3.101869708
#> AK1 SHANK1 PLK2 APBA1 GMPS
#> -3.111341359 -3.124920473 -3.148840285 -3.154339208 -3.159268973
#> BEND5 NRBF2 KCNE1 STK24 KCNJ11
#> -3.187631542 -3.197773230 -3.201637302 -3.231419800 -3.268724895
#> ACSBG1 SRI APRT BLVRB GPX1
#> -3.271629367 -3.272309868 -3.281613667 -3.286763324 -3.295510868
#> CYP19A1 ANOS1 GUCY2D TTK BRD8
#> -3.304959833 -3.308331432 -3.311517308 -3.313058779 -3.314277230
#> PTGES GPX7 DOK5 AKR1C4 ACIN1
#> -3.334931091 -3.347050720 -3.354222681 -3.396087245 -3.431602615
#> BMP8A CBR1 CYP2D6 FNBP1 MBOAT7
#> -3.457294980 -3.460027894 -3.467237466 -3.484591338 -3.506053361
#> ACSL4 ADAM23 DLD CDK17 CLIC6
#> -3.514122934 -3.570407847 -3.599095217 -3.628022789 -3.628435198
#> CYP7A1 SIK2 TACC2 PTGES2 ADAM22
#> -3.628577133 -3.634551011 -3.649108653 -3.661114157 -3.674395398
#> ADK ACP3 SLK CD7 ARL3
#> -3.683475066 -3.684533408 -3.705095905 -3.709705338 -3.780027934
#> ADSL AK2 MPO BRSK1 CDA
#> -3.785464836 -3.788907189 -3.815924086 -3.835560845 -3.842481691
#> EFHC1 NASP TSSK1B DDX19B SPR
#> -3.844235078 -3.855860289 -3.860830942 -3.865361825 -3.901644448
#> HSD17B8 CABP1 ADIPOR1 CES1 SRD5A3
#> -3.942820789 -3.957510427 -3.985970464 -4.002354016 -4.135839769
#> SPRR2D CYB5A TDRD7 SRD5A1 SRD5A2
#> -4.160201137 -4.186857163 -4.213670812 -4.221298390 -4.221298390
#> ACTR8 GUSB CYP27A1 MYO3A ARSA
#> -4.285894759 -4.303560928 -4.312825224 -4.403472228 -4.549120017
#> FDX1 SEMA3F DOLK RUFY1 KCNAB1
#> -4.565842777 -4.709603537 -4.740867768 -4.777998061 -4.816151889
#> MIR224 ALG10
#> -4.998846276 -5.146970852
Example 3. Calculate the consistency of the prediction
The function cronbach.alpha and kendall.w
are used to calculate the prediction consistency.
If you have several prediction results, you can use either function
to describe the consistency.
# Just report the results
kendall.w(data)$report
#> [1] "Kendall's coefficient W = 0.89, p = 0.0377"
# Or just report the alpha
cronbach.alpha(data)
#> [1] 0.8794233