Gene expression profiling in the developing secondary palate in the absence of Tbx1 function

Zoupa, Maria; Xavier, Guilherme Machado; Bryan, Stephanie; Theologidis, Ioannis; Arno, Matthew; Cobourne, Martyn T.

doi:10.1186/s12864-018-4782-y

BMC Genomics

Table 1 Group comparison of Tbx1^+/+, Tbx1^+/− and Tbx1^−/− palatal shelves

From: Gene expression profiling in the developing secondary palate in the absence of Tbx1 function

Gene ID	Gene symbol	Description	logFC	Fold Change
Group A: Genes differentially expressed in mutant compared to WT palates
14,462	Gata3	GATA binding protein 3	1,10	2,15
66894	Wwp2	WW domain containing E3 ubiquitin protein ligase 2	0,64	1,55
20466	Sin3a	transcriptional regulator, SIN3A (yeast)	0,45	1,37
27999	Fam3c	family with sequence similarity 3, member C	−0,43	−1,35
23,945	Mgll	monoglyceride lipase	−0,44	−1,36
22145	Tuba4a	tubulin, alpha 4A	−0,46	−1,38
23,945	Mgll	monoglyceride lipase	−0,46	−1,38
17286	Meox2	mesenchyme homeobox 2	− 0,48	− 1,39
227929	Cytip	cytohesin 1 interacting protein	−0,50	−1,41
21393	Tcap	titin-cap	−0,50	−1,42
13426	Dync1i1	dynein cytoplasmic 1 intermediate chain 1	−0,51	−1,42
231,633	Tmem119	transmembrane protein 119	−0,52	−1,43
21953	Tnni2	troponin I, skeletal, fast 2	−0,54	−1,46
27,273	Pdk4	pyruvate dehydrogenase kinase, isoenzyme 4	−0,54	−1,46
13,038	Ctsk	cathepsin K	−0,57	− 1,48
107765	Ankrd1	ankyrin repeat domain 1 (cardiac muscle)	−0,57	−1,49
17533	Mrc1	mannose receptor, C type 1	−0,59	−1,50
50796	Dmrt1	doublesex and mab-3 related transcription factor 1	−0,59	−1,51
72713	Angptl1	angiopoietin-like 1	−0,61	−1,53
13346	Des	desmin	−0,67	−1,59
12862	Cox6a2	cytochrome c oxidase subunit VIa polypeptide 2	−0,69	−1,61
56437	Rrad	Ras-related associated with diabetes	−0,71	−1,64
12608	Cebpb	CCAAT/enhancer binding protein (C/EBP), beta	−0,71	−1,64
14066	F3	coagulation factor III	−0,74	−1,67
50768	Dlc1	deleted in liver cancer 1	−0,74	− 1,67
12299	Cacng1	calcium channel, voltage-dependent, gamma subunit 1	−0,74	−1,67
76,757	Trdn	triadin	−0,76	−1,69
11475	Acta2	actin, alpha 2, smooth muscle, aorta	−0,76	− 1,69
12292	Cacna1s	calcium channel, voltage-dependent, L type, alpha 1S subunit	−0,76	−1,70
56012	Pgam2	phosphoglycerate mutase 2	−0,79	−1,73
67951	Tubb6	tubulin, beta 6 class V	−0,83	−1,78
11656	Alas2	aminolevulinic acid synthase 2, erythroid	−0,84	− 1,80
19400	Rapsn	receptor-associated protein of the synapse	−0,85	−1,80
22004	Tpm2	tropomyosin 2, beta	−0,86	−1,82
12575	Cdkn1a	cyclin-dependent kinase inhibitor 1A (P21)	−0,87	−1,83
17189	Mb	myoglobin	−0,88	−1,85
11609	Agtr2	angiotensin II receptor, type 2	−0,90	−1,86
21384	Tbx15	T-box 15	− 0,91	− 1,87
12955	Cryab	crystallin, alpha B	−0,92	−1,89
12955	Cryab	crystallin, alpha B	−0,92	−1,89
50795	Sh3bgr	SH3-binding domain glutamic acid-rich protein	−0,92	−1,89
17930	Myom2	myomesin 2	−0,95	−1,93
12180	Smyd1	SET and MYND domain containing 1	−0,96	−1,94
59058	Bhlhe22	basic helix-loop-helix family, member e22	−0,96	−1,95
26465	Zfp146	zinc finger protein 146	−1,01	−2,01
12391	Cav3	caveolin 3	−1,02	−2,02
65086	Lpar3	lysophosphatidic acid receptor 3	−1,06	−2,09
170812	Ahsp	alpha hemoglobin stabilizing protein	−1,09	−2,13
14,077	Fabp3	fatty acid binding protein 3, muscle and heart	−1,10	−2,15
11443	Chrnb1	cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)	−1,11	−2,16
17929	Myom1	myomesin 1	−1,14	−2,20
21953	Tnni2	troponin I, skeletal, fast 2	−1,16	−2,24
244954	Prss35	protease, serine 35	−1,19	−2,29
69253	Hspb2	heat shock protein 2	−1,20	−2,29
21957	Tnnt3	troponin T3, skeletal, fast	−1,23	−2,35
14619	Gjb2	gap junction protein, beta 2	−1,24	−2,36
13009	Csrp3	cysteine and glycine-rich protein 3	−1,30	−2,46
12,350	Car3	carbonic anhydrase 3	−1,37	−2,59
56069	Il17b	interleukin 17B	−1,37	−2,59
11811	Apobec2	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 2	−1,43	−2,69
11937	Atp2a1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	−1,46	−2,76
66139	Tmem8c	transmembrane protein 8C	−1,48	−2,78
51801	Ramp1	receptor (calcitonin) activity modifying protein 1	−1,56	−2,94
24131	Ldb3	LIM domain binding 3	−1,56	−2,94
16545	Kera	keratocan	−1,81	−3,51
140781	Myh7	myosin, heavy polypeptide 7, cardiac muscle, beta	−1,81	−3,51
21828	Thbs4	thrombospondin 4	−1,91	−3,75
13380	Dkk1	dickkopf homolog 1 (Xenopus laevis)	− 1,94	−3,83
21955	Tnnt1	troponin T1, skeletal, slow	−1,95	−3,87
58916	Myot	myotilin	−1,98	−3,95
17928	Myog	myogenin	−2,04	−4,12
21380	Tbx1	T-box 1	− 2,06	−4,16
53311	Mybph	myosin binding protein H	−2,06	−4,16
21952	Tnni1	troponin I, skeletal, slow 1	−2,26	−4,79
12,350	Car3	carbonic anhydrase 3	−2,31	−4,97
66402	Sln	sarcolipin	−2,40	−5,28
11472	Actn2	actinin alpha 2	−2,40	−5,29
17896	Myl4	myosin, light polypeptide 4	−2,44	−5,43
21956	Tnnt2	troponin T2, cardiac	−2,53	−5,77
11464	Actc1	actin, alpha, cardiac muscle 1	−2,56	−5,90
66106	Smpx	small muscle protein, X-linked	−2,61	−6,11
21924	Tnnc1	troponin C, cardiac/slow skeletal	−2,67	−6,35
17901	Myl1	myosin, light polypeptide 1	−2,76	−6,76
21925	Tnnc2	troponin C2, fast	−2,77	−6,83
17907	Mylpf	myosin light chain, phosphorylatable, fast skeletal muscle	−2,88	−7,35
21956	Tnnt2	troponin T2, cardiac	−2,92	−7,57
11459	Acta1	actin, alpha 1, skeletal muscle	−3,10	−8,60
17883	Myh3	myosin, heavy polypeptide 3, skeletal muscle, embryonic	−3,22	−9,29
15,891	Ibsp	integrin binding sialoprotein	−3,51	−11,36
Group C: Genes differentially expressed in mutant compared to heterozygous palates
12,846	Comt	catechol-O-methyltransferase	1,0	2,1
74,374	Clec16a	C-type lectin domain family 16, member A	0,8	1,8
54153	Rasa4	RAS p21 protein activator 4	0,7	1,6
66894	Wwp2	WW domain containing E3 ubiquitin protein ligase 2	0,6	1,5
18,155	Pnoc	prepronociceptin	0,6	1,5
56,538	Klk11	kallikrein related-peptidase 11	0,5	1,4
80904	Dtx3	deltex 3 homolog (Drosophila)	0,5	1,4
212,127	Proser1	proline and serine rich 1	0,5	1,4
108655	Foxp1	forkhead box P1	0,4	1,4
76501	Commd9	COMM domain containing 9	0,4	1,4
14809	Grik5	glutamate receptor, ionotropic, kainate 5 (gamma 2)	0,4	1,3
19280	Ptprs	protein tyrosine phosphatase, receptor type, S	−0,3	−1,3
18,008	Nes	nestin	−0,4	−1,3
27999	Fam3c	family with sequence similarity 3, member C	−0,4	−1,3
13426	Dync1i1	dynein cytoplasmic 1 intermediate chain 1	−0,4	−1,3
65114	Vps35	vacuolar protein sorting 35	−0,5	−1,4
21393	Tcap	titin-cap	−0,5	−1,4
17286	Meox2	mesenchyme homeobox 2	− 0,5	− 1,4
17286	Meox2	mesenchyme homeobox 2	− 0,5	− 1,4
72713	Angptl1	angiopoietin-like 1	−0,5	−1,4
67405	Nts	neurotensin	−0,6	− 1,5
11,303	Abca1	ATP-binding cassette, sub-family A (ABC1), member 1	−0,6	−1,5
21812	Tgfbr1	transforming growth factor, beta receptor I	−0,6	−1,5
15,366	Hmmr	hyaluronan mediated motility receptor (RHAMM)	−0,6	−1,5
11,733	Ank1	ankyrin 1, erythroid	−0,6	−1,5
21412	Tcf21	transcription factor 21	−0,6	−1,5
50796	Dmrt1	doublesex and mab-3 related transcription factor 1	−0,7	−1,6
12862	Cox6a2	cytochrome c oxidase subunit VIa polypeptide 2	−0,7	−1,6
50768	Dlc1	deleted in liver cancer 1	−0,7	−1,6
56437	Rrad	Ras-related associated with diabetes	−0,7	−1,6
56012	Pgam2	phosphoglycerate mutase 2	−0,7	−1,6
67951	Tubb6	tubulin, beta 6 class V	−0,7	−1,6
11,870	Art1	ADP-ribosyltransferase 1	−0,7	−1,7
15375	Foxa1	forkhead box A1	−0,7	−1,7
11,475	Acta2	actin, alpha 2, smooth muscle, aorta	−0,8	−1,7
12292	Cacna1s	calcium channel, voltage-dependent, L type, alpha 1S subunit	−0,8	−1,7
19400	Rapsn	receptor-associated protein of the synapse	−0,8	−1,7
80,882,479	Lrrn1	leucine rich repeat protein 1, neuronal	−0,8	−1,7
17189	Mb	myoglobin	−0,8	−1,7
12299	Cacng1	calcium channel, voltage-dependent, gamma subunit 1	−0,8	−1,8
12955	Cryab	crystallin, alpha B	−0,8	−1,8
11609	Agtr2	angiotensin II receptor, type 2	−0,9	−1,8
111,886,114	Cryab	crystallin, alpha B	−0,9	−1,8
17930	Myom2	myomesin 2	−0,9	−1,8
12180	Smyd1	SET and MYND domain containing 1	−0,9	−1,8
170812	Ahsp	alpha hemoglobin stabilizing protein	−0,9	−1,9
50795	Sh3bgr	SH3-binding domain glutamic acid-rich protein	−0,9	−1,9
14066	F3	coagulation factor III	−0,9	−1,9
59058	Bhlhe22	basic helix-loop-helix family, member e22	−1,0	−2,0
12391	Cav3	caveolin 3	−1,0	−2,1
17929	Myom1	myomesin 1	−1,1	−2,1
26465	Zfp146	zinc finger protein 146	−1,1	−2,1
21384	Tbx15	T-box 15	− 1,1	−2,1
21384	Tbx15	T-box 15	− 1,1	−2,2
11443	Chrnb1	cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)	−1,1	−2,2
21953	Tnni2	troponin I, skeletal, fast 2	−1,2	−2,2
69253	Hspb2	heat shock protein 2	−1,2	−2,2
13009	Csrp3	cysteine and glycine-rich protein 3	−1,2	−2,3
21957	Tnnt3	troponin T3, skeletal, fast	−1,3	−2,4
11937	Atp2a1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	−1,3	−2,4
56069	Il17b	interleukin 17B	−1,3	−2,5
14619	Gjb2	gap junction protein, beta 2	−1,5	−2,8
11435	Chrna1	cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)	−1,5	−2,8
11811	Apobec2	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 2	−1,5	−2,9
24131	Ldb3	LIM domain binding 3	−1,6	−3,0
17927	Myod1	myogenic differentiation 1	−1,6	−3,1
66139	Tmem8c	transmembrane protein 8C	−1,7	−3,2
21828	Thbs4	thrombospondin 4	−1,8	−3,4
140781	Myh7	myosin, heavy polypeptide 7, cardiac muscle, beta	−1,9	−3,7
58916	Myot	myotilin	−2,0	−3,9
87,201,087	Tnnt1	troponin T1, skeletal, slow	−2,0	−3,9
17928	Myog	myogenin	−2,1	−4,3
53311	Mybph	myosin binding protein H	−2,2	−4,5
21952	Tnni1	troponin I, skeletal, slow 1	−2,4	−5,3
11,472	Actn2	actinin alpha 2	−2,4	−5,4
17896	Myl4	myosin, light polypeptide 4	−2,5	−5,5
66,402	Sln	sarcolipin	−2,5	−5,5
21,380	Tbx1	T-box 1	−2,6	−6,1
21956	Tnnt2	troponin T2, cardiac	−2,6	−6,2
66106	Smpx	small muscle protein, X-linked	−2,7	−6,5
11464	Actc1	actin, alpha, cardiac muscle 1	−2,7	−6,5
92,760,598	Tnnc1	troponin C, cardiac/slow skeletal	−2,7	−6,6
21925	Tnnc2	troponin C2, fast	−2,8	−6,9
17901	Myl1	myosin, light polypeptide 1	−2,8	−7,2
17907	Mylpf	myosin light chain, phosphorylatable, fast skeletal muscle	−3,0	−7,9
80,608,559	Tnnt2	troponin T2, cardiac	−3,1	−8,5
11,459	Acta1	actin, alpha 1, skeletal muscle	−3,1	−8,7
17883	Myh3	myosin, heavy polypeptide 3, skeletal muscle, embryonic	−3,2	−9,3

Genes are listed based on fold change

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