Mutation Analysis (MutSig v1.5) - Acute Myeloid Leukemia (Primary blood derived cancer

Mutation Analysis (MutSig v1.5)

Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)

23 May 2013 | analyses__2013_05_23

Maintainer Information

Citation Information

Maintained by Dan DiCara (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig v1.5). Broad Institute of MIT and Harvard. doi:10.7908/C1765CCP

- Overview

+ Introduction

- Summary

MAF used for this analysis:LAML-TB.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 28
Mutations seen in COSMIC: 238
Significantly mutated genes in COSMIC territory: 19
Genes with clustered mutations (≤ 3 aa apart): 18
Significantly mutated genesets: 69
Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing

Read 197 MAFs of type "WashU"
Total number of mutations in input MAFs: 2585
After removing 41 mutations outside chr1-24: 2544
After removing 1 blacklisted mutations: 2543
After removing 104 noncoding mutations: 2439

Mutation Filtering

Number of mutations before filtering: 2439
After removing 204 mutations outside gene set: 2235
After removing 14 mutations outside category set: 2221

- Results

+ Breakdown of Mutations by Type

type	count
Frame_Shift_Del	51
Frame_Shift_Ins	110
In_Frame_Del	8
In_Frame_Ins	43
Missense_Mutation	1401
Nonsense_Mutation	108
Silent	450
Splice_Site	50
Total	2221

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate
*CpG->T	509	272310736	1.9e-06	1.9	5.8
*Cp(A/C/T)->T	312	2468091057	1.3e-07	0.13	0.39
A->G	182	2745259222	6.6e-08	0.066	0.21
transver	398	5485661015	7.3e-08	0.073	0.22
indel+null	357	5485661212	6.5e-08	0.065	0.2
double_null	13	5485661212	2.4e-09	0.0024	0.0073
Total	1771	5485661212	3.2e-07	0.32	1

+ Target Coverage for Each Individual

+ Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples

+ CoMut Plot

+ Significantly Mutated Genes

Column Descriptions:

N = number of sequenced bases in this gene across the individual set
n = number of (nonsilent) mutations in this gene across the individual set
npat = number of patients (individuals) with at least one nonsilent mutation
nsite = number of unique sites having a non-silent mutation
nsil = number of silent mutations in this gene across the individual set
n1 = number of nonsilent mutations of type: *CpG->T
n2 = number of nonsilent mutations of type: *Cp(A/C/T)->T
n3 = number of nonsilent mutations of type: A->G
n4 = number of nonsilent mutations of type: transver
n5 = number of nonsilent mutations of type: indel+null
n6 = number of nonsilent mutations of type: double_null
p = p-value (overall)
q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 28. Number of genes displayed: 35. Click on a gene name to display its stick figure depicting the distribution of mutations and mutation types across the chosen gene (this feature may not be available for all significant genes).

rank	gene	description	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p	q
1	NPM1	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	183407	54	54	7	0	0	0	1	0	52	1	<1.00e-15	<3.84e-12
2	IDH1	isocitrate dehydrogenase 1 (NADP+), soluble	251569	19	19	2	0	17	0	0	2	0	0	<1.00e-15	<3.84e-12
3	RUNX1	runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene)	145189	20	18	16	0	2	3	2	2	10	1	<1.00e-15	<3.84e-12
4	TP53	tumor protein p53	258267	18	15	18	1	3	2	3	2	8	0	<1.00e-15	<3.84e-12
5	DNMT3A	DNA (cytosine-5-)-methyltransferase 3 alpha	512791	57	51	29	0	34	2	3	4	14	0	1.11e-15	3.84e-12
6	IDH2	isocitrate dehydrogenase 2 (NADP+), mitochondrial	230293	20	20	2	0	16	3	0	1	0	0	3.89e-15	1.12e-11
7	WT1	Wilms tumor 1	164692	12	12	10	0	1	1	0	0	9	1	6.00e-15	1.26e-11
8	FLT3	fms-related tyrosine kinase 3	597107	56	56	30	0	0	0	1	16	39	0	6.55e-15	1.26e-11
9	TET2	tet oncogene family member 2	689894	21	17	20	0	0	2	0	2	11	6	6.55e-15	1.26e-11
10	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	115442	15	15	6	0	0	8	1	6	0	0	1.09e-14	1.88e-11
11	PTPN11	protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1)	359328	9	9	9	0	0	3	2	4	0	0	1.32e-14	2.07e-11
12	U2AF1	U2 small nuclear RNA auxiliary factor 1	153266	8	8	2	0	0	5	0	3	0	0	1.45e-14	2.09e-11
13	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	139279	8	8	6	0	0	4	1	3	0	0	2.28e-14	3.02e-11
14	KIT	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	585287	9	8	5	0	1	0	0	6	1	1	1.02e-11	1.26e-08
15	PHF6	PHD finger protein 6	244083	6	6	6	0	0	1	0	1	4	0	4.17e-11	4.80e-08
16	SMC3	structural maintenance of chromosomes 3	738947	7	7	7	0	1	1	1	2	2	0	1.54e-09	1.66e-06
17	SMC1A	structural maintenance of chromosomes 1A	744857	7	7	7	0	3	0	1	2	1	0	4.85e-09	4.93e-06
18	RAD21	RAD21 homolog (S. pombe)	383756	5	5	5	0	0	0	0	0	5	0	6.34e-08	6.08e-05
19	STAG2	stromal antigen 2	775983	6	6	6	0	0	0	0	0	6	0	8.03e-08	7.30e-05
20	FAM5C	family with sequence similarity 5, member C	458813	6	5	6	0	4	1	0	1	0	0	2.23e-07	0.000193
21	CBFB	core-binding factor, beta subunit	87862	2	2	2	0	0	0	0	0	2	0	8.73e-06	0.00718
22	ASXL1	additional sex combs like 1 (Drosophila)	903245	5	5	5	0	0	0	0	0	5	0	1.14e-05	0.00894
23	SUZ12	suppressor of zeste 12 homolog (Drosophila)	395182	3	3	3	0	1	1	0	0	1	0	8.84e-05	0.0664
24	DIS3	DIS3 mitotic control homolog (S. cerevisiae)	537613	3	3	3	0	1	1	1	0	0	0	0.000104	0.0742
25	PHACTR1	phosphatase and actin regulator 1	323868	3	3	2	0	0	0	0	1	2	0	0.000111	0.0742
26	EZH2	enhancer of zeste homolog 2 (Drosophila)	459010	3	3	3	0	1	0	0	0	1	1	0.000113	0.0742
27	GBP4	guanylate binding protein 4	387499	3	3	3	0	0	2	0	1	0	0	0.000116	0.0742
28	BAGE4	B melanoma antigen family, member 4	24822	1	1	1	0	1	0	0	0	0	0	0.000133	0.0821
29	CALR	calreticulin	218670	2	2	2	0	0	0	0	0	2	0	0.000187	0.111
30	CLEC18B	C-type lectin domain family 18, member B	209805	2	2	1	0	0	0	2	0	0	0	0.000231	0.133
31	FAM57B	family with sequence similarity 57, member B	77618	2	2	2	0	1	0	0	0	1	0	0.000248	0.138
32	ABTB1	ankyrin repeat and BTB (POZ) domain containing 1	176512	2	2	1	0	0	0	0	0	2	0	0.000301	0.155
33	KCNK13	potassium channel, subfamily K, member 13	176709	2	2	2	0	0	0	0	1	1	0	0.000304	0.155
34	GRIK2	glutamate receptor, ionotropic, kainate 2	560071	3	3	3	0	1	1	1	0	0	0	0.000306	0.155
35	MTA2	metastasis associated 1 family, member 2	403259	2	2	2	0	0	0	2	0	0	0	0.000345	0.170

+ COSMIC analyses

rank	gene	description	n	cos	n_cos	N_cos	cos_ev	p	q
1	TP53	tumor protein p53	18	824	16	162328	3427	0	0
2	IDH1	isocitrate dehydrogenase 1 (NADP+), soluble	19	5	19	985	28348	5.2e-14	9.1e-11
3	IDH2	isocitrate dehydrogenase 2 (NADP+), mitochondrial	20	6	20	1182	2000	6.3e-14	9.1e-11
4	PTPN11	protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1)	9	32	8	6304	216	3.3e-13	3e-10
5	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	15	33	15	6501	11840	3.4e-13	3e-10
6	NPM1	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	54	41	53	8077	112668	4.3e-13	3.1e-10
7	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	8	52	7	10244	46308	5.4e-13	3.4e-10
8	FLT3	fms-related tyrosine kinase 3	56	124	52	24428	6301	1.3e-12	7e-10
9	RUNX1	runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene)	20	178	18	35066	93	1.8e-12	8.3e-10
10	WT1	Wilms tumor 1	12	185	9	36445	444	1.9e-12	8.3e-10

+ Clustered Mutations

num	gene	desc	n	nmuts0	nmuts3	nmuts12	npairs0	npairs3	npairs12
337	DNMT3A	DNA (cytosine-5-)-methyltransferase 3 alpha	57	408	410	427	408	410	427
535	IDH1	isocitrate dehydrogenase 1 (NADP+), soluble	19	171	171	171	171	171	171
536	IDH2	isocitrate dehydrogenase 2 (NADP+), mitochondrial	20	139	139	139	139	139	139
429	FLT3	fms-related tyrosine kinase 3	55	120	120	136	120	120	136
752	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	15	31	51	51	31	51	51
955	RUNX1	runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene)	20	16	21	26	16	21	26
589	KIT	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	9	10	10	10	10	10	10
598	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	8	3	7	7	3	7	7
902	PTPN11	protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1)	9	1	3	10	1	3	10
1109	TET2	tet oncogene family member 2	21	1	1	2	1	1	2

+ Geneset Analyses

Table 6. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 69. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p	q
1	HSA00480_GLUTATHIONE_METABOLISM	Genes involved in glutathione metabolism	ANPEP, G6PD, GCLC, GCLM, GGT1, GGTL3, GGTL4, GPX1, GPX2, GPX3, GPX4, GPX5, GPX6, GPX7, GSR, GSS, GSTA1, GSTA2, GSTA3, GSTA4, GSTA5, GSTK1, GSTM1, GSTM2, GSTM3, GSTM4, GSTM5, GSTO2, GSTP1, GSTT1, GSTT2, GSTZ1, IDH1, IDH2, MGST1, MGST2, MGST3, OPLAH, TXNDC12	34	GCLM(1), GPX2(1), GSTK1(2), GSTM3(1), IDH1(19), IDH2(20)	5770918	44	42	9	0	34	4	0	6	0	0	<1.00e-15	<2.05e-13
2	GLUTATHIONE_METABOLISM		ANPEP, G6PD, GCLC, GCLM, GGT1, GPX1, GPX2, GPX3, GPX4, GPX5, GSS, GSTA1, GSTA2, GSTA3, GSTA4, GSTM1, GSTM2, GSTM3, GSTM4, GSTM5, GSTO2, GSTP1, GSTT1, GSTT2, GSTZ1, IDH1, IDH2, MGST1, MGST2, MGST3, PGD	29	GCLM(1), GPX2(1), GSTM3(1), IDH1(19), IDH2(20)	5170462	42	40	7	0	33	4	0	5	0	0	<1.00e-15	<2.05e-13
3	HSA04060_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION	Genes involved in cytokine-cytokine receptor interaction	ACVR1, ACVR1B, ACVR2A, ACVR2B, AMH, AMHR2, BMP2, BMP7, BMPR1A, BMPR1B, BMPR2, CCL1, CCL11, CCL13, CCL14, CCL15, CCL16, CCL17, CCL18, CCL19, CCL2, CCL20, CCL21, CCL22, CCL23, CCL24, CCL25, CCL26, CCL27, CCL28, CCL3, CCL4, CCL5, CCL7, CCL8, CCR1, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CD27, CD40, CD40LG, CD70, CLCF1, CNTF, CNTFR, CRLF2, CSF1, CSF1R, CSF2, CSF2RA, CSF2RB, CSF3, CSF3R, CTF1, CX3CL1, CX3CR1, CXCL1, CXCL10, CXCL11, CXCL12, CXCL13, CXCL14, CXCL16, CXCL2, CXCL3, CXCL5, CXCL6, CXCL9, CXCR3, CXCR4, CXCR6, EDA, EDA2R, EDAR, EGF, EGFR, EPO, EPOR, FAS, FASLG, FLJ78302, FLT1, FLT3, FLT3LG, FLT4, GDF5, GH1, GH2, GHR, HGF, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNAR1, IFNAR2, IFNB1, IFNE1, IFNG, IFNGR1, IFNGR2, IFNK, IFNW1, IL10, IL10RA, IL10RB, IL11, IL11RA, IL12A, IL12B, IL12RB1, IL12RB2, IL13, IL13RA1, IL15, IL15RA, IL17A, IL17B, IL17RA, IL17RB, IL18, IL18R1, IL18RAP, IL19, IL1A, IL1B, IL1R1, IL1R2, IL1RAP, IL2, IL20, IL20RA, IL21, IL21R, IL22, IL22RA1, IL22RA2, IL23A, IL23R, IL24, IL25, IL26, IL28A, IL28B, IL28RA, IL29, IL2RA, IL2RB, IL2RG, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL6ST, IL7, IL7R, IL8, IL8RA, IL8RB, IL9, IL9R, INHBA, INHBB, INHBC, INHBE, KDR, KIT, KITLG, LEP, LEPR, LIF, LIFR, LOC728045, LTA, LTB, LTBR, MET, MPL, NGFR, OSM, OSMR, PDGFB, PDGFC, PDGFRA, PDGFRB, PF4, PF4V1, PLEKHO2, PPBP, PRL, PRLR, RELT, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFRSF11A, TNFRSF11B, TNFRSF12A, TNFRSF13B, TNFRSF13C, TNFRSF14, TNFRSF17, TNFRSF18, TNFRSF19, TNFRSF1A, TNFRSF1B, TNFRSF21, TNFRSF25, TNFRSF4, TNFRSF6B, TNFRSF8, TNFRSF9, TNFSF10, TNFSF11, TNFSF12, TNFSF13, TNFSF13B, TNFSF14, TNFSF15, TNFSF18, TNFSF4, TNFSF8, TNFSF9, TPO, TSLP, VEGFA, VEGFB, VEGFC, XCL1, XCL2, XCR1	242	ACVR2B(1), CCL11(1), CCL16(1), CCL20(1), CCL21(1), CD70(1), CSF3R(1), EGFR(2), FLT1(1), FLT3(56), IL1R1(1), KDR(2), KIT(9), MPL(1), PDGFRA(1), PDGFRB(1), TPO(1)	49587855	82	78	52	4	7	5	2	27	40	1	1.22e-15	2.05e-13
4	HSA00271_METHIONINE_METABOLISM	Genes involved in methionine metabolism	AHCY, AMD1, BHMT, CBS, CTH, DNMT1, DNMT3A, DNMT3B, KIAA0828, MARS, MARS2, MAT1A, MAT2B, MTAP, MTFMT, MTR, SRM, TAT	17	DNMT1(1), DNMT3A(57), DNMT3B(1), MAT1A(1)	5703150	60	53	32	0	36	2	3	5	14	0	1.33e-15	2.05e-13
5	NUCLEAR_RECEPTORS		ALK, AR, ESR1, ESR2, ESRRA, HNF4A, NPM1, NR0B1, NR1D2, NR1H2, NR1H3, NR1I2, NR1I3, NR2C2, NR2E1, NR2F1, NR2F2, NR2F6, NR3C1, NR4A1, NR4A2, NR5A1, NR5A2, PGR, PPARA, PPARD, PPARG, RARA, RARB, RARG, ROR1, RORA, RORC, RXRA, RXRB, RXRG, THRA, THRA, NR1D1, THRB, VDR	38	NPM1(54), NR2E1(2), THRB(1)	11589707	57	56	10	0	1	1	1	1	52	1	2.11e-15	2.25e-13
6	HSA04640_HEMATOPOIETIC_CELL_LINEAGE	Genes involved in hematopoietic cell lineage	ANPEP, CD14, CD19, CD1A, CD1B, CD1C, CD1D, CD1E, CD2, CD22, CD24, CD33, CD34, CD36, CD37, CD38, CD3D, CD3E, CD3G, CD4, CD44, CD5, CD55, CD59, CD7, CD8A, CD8B, CD9, CR1, CR2, CSF1, CSF1R, CSF2, CSF2RA, CSF3, CSF3R, DNTT, EPO, EPOR, FCER2, FCGR1A, FLT3, FLT3LG, GP1BA, GP1BB, GP5, GP9, GYPA, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, IL11, IL11RA, IL1A, IL1B, IL1R1, IL1R2, IL2RA, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL7, IL7R, IL9R, ITGA1, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGAM, ITGB3, KIT, KITLG, MME, MS4A1, TFRC, THPO, TNF, TPO	83	CR1(1), CSF3R(1), FLT3(56), HLA-DRB1(1), IL1R1(1), KIT(9), TPO(1)	23989281	70	68	40	1	2	2	1	24	40	1	2.44e-15	2.25e-13
7	HSA00720_REDUCTIVE_CARBOXYLATE_CYCLE	Genes involved in reductive carboxylate cycle (CO2 fixation)	ACLY, ACO1, ACO2, ACSS1, ACSS2, FH, IDH1, IDH2, LOC441996, MDH1, MDH2, SUCLA2	11	IDH1(19), IDH2(20)	3866716	39	38	4	0	33	3	0	3	0	0	2.55e-15	2.25e-13
8	METHIONINE_METABOLISM		AHCY, BHMT, CBS, CTH, DNMT1, DNMT2, DNMT3A, DNMT3B, MARS, MARS2, MAT1A, MAT2B, MTR	12	DNMT1(1), DNMT3A(57), DNMT3B(1), MAT1A(1)	4841078	60	53	32	0	36	2	3	5	14	0	3.11e-15	2.39e-13
9	REDUCTIVE_CARBOXYLATE_CYCLE_CO2_FIXATION		ACO1, ACO2, FH, IDH1, IDH2, MDH1, MDH2, SDHB, SUCLA2	9	IDH1(19), IDH2(20)	2582079	39	38	4	0	33	3	0	3	0	0	3.55e-15	2.43e-13
10	KREBPATHWAY	The Krebs (citric acid) cycle takes place in mitochondria, where it extracts energy in the form of electron carriers NADH and FADH2, which drive the electron transport chain.	ACO2, CS, FH, IDH2, MDH1, OGDH, SDHA, SUCLA2	8	IDH2(20)	2741649	20	20	2	0	16	3	0	1	0	0	4.66e-15	2.47e-13

Table 7. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 0. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	p	q
1	SPRYPATHWAY	Four members of the Sprouty protein family block proliferative EGF signals by binding Grb-2, preventing Ras and MAP kinase activation.	CBL, EGF, EGFR, GRB2, HRAS, MAP2K1, MAPK1, MAPK3, PTPRB, RAF1, RASA1, SHC1, SOS1, SPRY1, SPRY2, SPRY3, SPRY4, SRC	18	CBL(2), EGFR(2), MAPK1(1), SHC1(1), SOS1(1)	7219656	7	7	7	2	2	1	1	1	2	0.0031	1
2	ERKPATHWAY	Cell growth is promoted by Ras activation of the anti-apoptotic p44/42 MAP kinase pathway.	DPM2, EGFR, ELK1, GNAS, GNB1, GNGT1, GRB2, HRAS, IGF1R, ITGB1, KLK2, MAP2K1, MAP2K2, MAPK1, MAPK3, MKNK1, MKNK2, MYC, NGFB, NGFR, PDGFRA, PPP2CA, PTPRR, RAF1, RPS6KA1, RPS6KA5, SHC1, SOS1, SRC, STAT3	28	EGFR(2), GNB1(1), MAPK1(1), MYC(1), PDGFRA(1), SHC1(1), SOS1(1)	9060424	8	8	8	1	3	1	0	3	1	0.0057	1
3	EOSINOPHILSPATHWAY	Recruitment of eosinophils in the inflammatory response observed in asthma occurs via the chemoattractant eotaxin binding to the CCR3 receptor.	CCL11, CCL5, CCR3, CSF2, HLA-DRA, HLA-DRB1, IL3, IL5	8	CCL11(1), HLA-DRB1(1)	893001	2	2	2	0	0	1	0	1	0	0.015	1
4	HSA00480_GLUTATHIONE_METABOLISM	Genes involved in glutathione metabolism	ANPEP, G6PD, GCLC, GCLM, GGT1, GGTL3, GGTL4, GPX1, GPX2, GPX3, GPX4, GPX5, GPX6, GPX7, GSR, GSS, GSTA1, GSTA2, GSTA3, GSTA4, GSTA5, GSTK1, GSTM1, GSTM2, GSTM3, GSTM4, GSTM5, GSTO2, GSTP1, GSTT1, GSTT2, GSTZ1, IDH1, IDH2, MGST1, MGST2, MGST3, OPLAH, TXNDC12	32	GCLM(1), GPX2(1), GSTK1(2), GSTM3(1)	5289056	5	5	5	0	1	1	0	3	0	0.017	1
5	HSA04080_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION	Genes involved in neuroactive ligand-receptor interaction	ADCYAP1R1, ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA2A, ADRA2B, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BRS3, C3AR1, C5AR1, CALCR, CALCRL, CCKAR, CCKBR, CGA, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CNR1, CNR2, CRHR1, CRHR2, CTSG, CYSLTR1, CYSLTR2, DRD1, DRD2, DRD3, DRD4, DRD5, EDG1, EDG2, EDG3, EDG4, EDG5, EDG6, EDG7, EDG8, EDNRA, EDNRB, F2, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHB, FSHR, GABBR1, GABBR2, GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GABRB1, GABRB2, GABRB3, GABRD, GABRE, GABRG1, GABRG2, GABRG3, GABRP, GABRQ, GABRR1, GABRR2, GALR1, GALR2, GALR3, GCGR, GH1, GH2, GHR, GHRHR, GHSR, GIPR, GLP1R, GLP2R, GLRA1, GLRA2, GLRA3, GLRB, GNRHR, GPR156, GPR23, GPR35, GPR50, GPR63, GPR83, GRIA1, GRIA2, GRIA3, GRIA4, GRID1, GRID2, GRIK1, GRIK2, GRIK3, GRIK4, GRIK5, GRIN1, GRIN2A, GRIN2B, GRIN2C, GRIN2D, GRIN3A, GRIN3B, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GRPR, GZMA, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HRH4, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, KISS1R, LEP, LEPR, LHB, LHCGR, LTB4R, LTB4R2, MAS1, MC1R, MC2R, MC3R, MC4R, MC5R, MCHR1, MCHR2, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPBWR1, NPBWR2, NPFFR1, NPFFR2, NPY1R, NPY2R, NPY5R, NR3C1, NTSR1, NTSR2, OPRD1, OPRK1, OPRL1, OPRM1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, P2RY1, P2RY10, P2RY11, P2RY13, P2RY14, P2RY2, P2RY4, P2RY5, P2RY6, P2RY8, PARD3, PPYR1, PRL, PRLHR, PRLR, PRSS1, PRSS2, PRSS3, PTAFR, PTGDR, PTGER1, PTGER2, PTGER3, PTGER4, PTGFR, PTGIR, PTH2R, PTHR1, RXFP1, RXFP2, SCTR, SSTR1, SSTR2, SSTR3, SSTR4, SSTR5, TAAR1, TAAR2, TAAR5, TAAR6, TAAR8, TAAR9, TACR1, TACR2, TACR3, TBXA2R, THRA, THRB, TRHR, TRPV1, TSHB, TSHR, TSPO, UTS2R, VIPR1, VIPR2	220	BRS3(1), CTSG(1), DRD2(1), GABBR1(1), GABRA4(1), GABRB1(1), GABRG2(1), GABRR1(1), GLRA1(1), GNRHR(1), GRID1(2), GRIK2(3), GRIK3(1), GRIK4(2), GRM3(2), GRM8(2), HTR5A(1), MCHR2(1), NMUR2(2), NTSR2(1), OPRM1(1), P2RY2(2), PARD3(1), PRSS3(1), SCTR(1), SSTR4(1), THRB(1), VIPR1(1)	60360209	36	30	36	9	17	7	2	9	1	0.023	1
6	ST_G_ALPHA_I_PATHWAY	Gi and Go proteins are members of the same family that transduce cellular signals through both their alpha and beta subunits.	AKT1, AKT2, AKT3, ASAH1, BF, BRAF, DAG1, DRD2, EGFR, EPHB2, GRB2, ITPKA, ITPKB, ITPR1, ITPR2, ITPR3, KCNJ3, KCNJ5, KCNJ9, MAPK1, PI3, PIK3CB, PITX2, PLCB1, PLCB2, PLCB3, PLCB4, RAF1, RAP1GA1, RGS20, SHC1, SOS1, SOS2, SRC, STAT3, TERF2IP	33	DAG1(1), DRD2(1), EGFR(2), ITPR1(1), ITPR3(1), MAPK1(1), PIK3CB(1), SHC1(1), SOS1(1)	16836802	10	10	10	4	3	5	0	1	1	0.025	1
7	IL2RBPATHWAY	The beta subunit of the IL-2 receptor is required for IL-2 and IL-15 signal recognition and activates JAK kinase on ligand binding.	AKT1, BAD, BCL2, BCL2L1, CBL, CFLAR, CRKL, E2F1, FOS, GRB2, HRAS, IL2RA, IL2RB, IL2RG, IRS1, JAK1, JAK3, MAPK1, MAPK3, MYC, NMI, PIK3CA, PIK3R1, PPIA, PTPN6, RAF1, RPS6KB1, SHC1, SOCS1, SOCS3, SOS1, STAT5A, STAT5B, SYK, TNFRSF6, TNFSF6, ZNFN1A3	33	CBL(2), JAK3(1), MAPK1(1), MYC(1), SHC1(1), SOS1(1)	10266655	7	7	7	3	2	2	1	0	2	0.026	1
8	CBLPATHWAY	Activated EGF receptors undergo endocytosis into clathrin-coated vesicles, where they are recycled to the membrane or ubiquitinated by Cbl.	CBL, CSF1R, EGF, EGFR, GRB2, MET, PDGFRA, PRKCA, PRKCB1, SH3GLB1, SH3GLB2, SH3KBP1, SRC	12	CBL(2), EGFR(2), PDGFRA(1)	5655476	5	5	5	1	1	0	1	2	1	0.026	1
9	CLASSICPATHWAY	The classic complement pathway is initiated by antibodies and promotes phagocytosis and lysis of foreign cells as well as activating the inflammatory response.	C1QA, C1QB, C1QG, C1R, C1S, C2, C3, C4A, C4B, C5, C6, C7, C8A, C9	11	C2(1), C3(1), C5(1), C7(1)	5092647	4	4	4	1	2	0	0	1	1	0.026	1
10	ALTERNATIVEPATHWAY	The alternative complement pathway is an antibody-independent mechanism of immune activation that results in cell lysis via the membrane attack complex.	BF, C3, C5, C6, C7, C8A, C9, DF, PFC	6	C3(1), C5(1), C7(1)	3564715	3	3	3	1	1	0	0	1	1	0.027	1

+ Methods & Data

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