7 8 9 9 10 11 1 TONSL vs Primary log2FPKM Raw counts 2 foldchange log2FC PValue KTB_103_pr KTB103_prir KTB103_prir KTB_103_TC KTB_103_TC KTB_103_TCKTB_103_pr KTB103_prir KTB103_prir KTB_103_TC KTB_103_TC KTB_103_TONSL-F_S22 3 3604.4176 11.81555 2.85E-284 1.55E-282-9.3129082 -9.3129082 -9.3129082 1.4648813 1.5160533 1.5272297 0315000 6 4 1099.1348 10.102153 4.99E-95 5.49E-94 -9.32157 -9.32157 -9.32157 -0.0733843 -0.3162863 -0.2790863 5 847.28604 9.7267053 1.49E-77 1.33E-76 -8.215888 -8.215888 -8.215888 0.631853 0.3966124 0.4940631 204 64000 6500306 memo 9.3744036 791.81993 9.6290286 8.59E-75 7.38E-74 -8.2711026 -8.2711026 -8.2711026 0.4262034 0.3831127 0.2707696 136.06836 EASDEES 726.06516 9.5039552 2.36E-69 1.87E-68 -6.8822306 -6.8822306 -6.8822306 1.5912286 1.7160924 1.5676387 600 4400302402006 4.36.363 ******* 2443603 **** 100*50*5.240*30 33103836 608.11897 9.2482098 1.2E-267 5.95E-266-7.9296227 -4.7142693 -7.9296227 2.9934394 3.2481759 3.2192825 www.c SERVEET MUO *600*65 0.0384336 0.000000 ***************** 456.80467 8.8354336 2.38E-43 -9.090888 -9.090888 -9.090888 -1.1241791 -1.4468333 -1.2171597 www.www 0:0934350 6104343 404247 076474 4064376* $0413500 C10423 384.39701 8.5864533 3.782E-39 1.792E-38 -9.5491347 -9.5491347 -9.5491347 -1.975471 -1.9613751 -1.9412599 www 367.82505 8.5228759 2.41E-37 11367.62505 6.5226159 ZNIES! 346.01397 8.4346865 1.09E-117 340.01997 0340009 4.56E-44 12 13 299.68622 8.2273089 4.24E-31 14 278.67084 8.1224182 3.13E-94 17 239.98475 7.9067989 4.70E-123 18 18 238.77865 1.10E-36 -8.6796094 -8.6796094 -8.6796094 -1.0796112 -1.2430199 -1.1466266 196094 -8.6796094 -1.0796112 -1.2430199 -1.1466266 BUCO HO 1.53E-116 -6.2563842 -8.8207137 -8.8207137 0.5240714 0.6412797 0.7507498 1.53E-110 -6.2563642 -6.8207137 -8.8207137 0.5240714 0.6412797 0.7507498 1.66E-30 -8.3760452 -8.3760452 -8.3760452 -1.1290682 -1.181848 -1.125163 -1.101646 -1.125163 3.41E-93-6.5188956 -6.5188956 -3.9634506 2.7864228 2.5182696 2.5766006 15 277.74252 8.1176043 1.11E-252 4.89E-251 -4.824966 -5.8989967 -5.7064293 2.602651 2.6864677 2.481924 16 10 259.38227 8.0189361 1.16E-26 4.07E-26 -8.4181912 -8.4181912 -8.4181912 -1.4660267 -1.5624062 -1.1988073 6.92E-122 -8.0754611 -4.8601077 -8.0754611 1.840504 1.6763788 1.4771684 -2.578528 1.86E-24 -6.424638 0.3993354 0.5234777 -6.424638 -6.424638 0475226 0.475236 6.0519258 1260692 04505629 02011205 2.06E-76 -8.6073708 -8.6073708 -6.0519258 0.1260692 0.4506639 0.2011305 3.26E-23 -9.1944906 -9.1944906 -9.1944906 -2.326509 -2.5992509 -2.21725 9.24E-133 -8.5795786 -8.5795786 -5.1523782 1.0913564 1.0728451 0.9667178 2.43E-22 -5.4410844 -5.4410844 -5.4410844 1.382889 1.035158 1.5361562 1.49E-21 -8.2515508 -8.2515508 -8.2515508 -1.1444625 -1.5463855 -1.8165229 2.19E-22 -9.8659117 -9.8659117 -9.8659117 -3.0419383 -3.0586068 -3.2266579 7.89953 19 236.26536 7.8842643 4485-24-9 5176038 -9 5176038 -9 5176038 -2.8844576 -2.4008619 20 330 12216 229.13316 7 8400424 1.36E-24 5.56E-25 7.8400424 2.31E-77 226.52461 7.823524 1.01E-23 220.17798 7.7825264 5.61E-134 219.35572 7.7771285 7.71E-23 21 22 22 23 24 217.6387 7.7657913 4.81E-22 25 215.16056 7.7492699 6.93E-23 DE_analysis + < H > K FDR R I 0 0 0 0 0 = 0 = 0 9 0 9 0 9 1 2 0 9 0 0 2 2 0 0 0 O 0 O 0 0 0 0 0 0 0 0 ◄ 0 0 0 0 0 = 2 • 0 9 0 9 0 9 0 9 0 0 0 1 + 0 2 0 0 O 0 0 0 0 0 O 0 0 0 0 0 0 0 = 0 0 = 0 9 0 9 0 9 0 9 0 0 1 ↓ 1 0 0 0 0 0 1 1 O 0 2 2 0 0 0 500 173 131 118 *** 101 553 71 54 55 185 43 180 531 35 275 28 32 121 33 232 32 39 32 475 134 102 105 101 *v* 605 52 50 45 43 184 38 137 516 30 225 36 32 139 25 210 23 27 29 557 160 127 113 106 690 71 2 59 34 56 30 231 46 166 521 45 228 37 36 36 136 38 227 38 26 30
7 8 9 9 10 11 1 TONSL vs Primary log2FPKM Raw counts 2 foldchange log2FC PValue KTB_103_pr KTB103_prir KTB103_prir KTB_103_TC KTB_103_TC KTB_103_TCKTB_103_pr KTB103_prir KTB103_prir KTB_103_TC KTB_103_TC KTB_103_TONSL-F_S22 3 3604.4176 11.81555 2.85E-284 1.55E-282-9.3129082 -9.3129082 -9.3129082 1.4648813 1.5160533 1.5272297 0315000 6 4 1099.1348 10.102153 4.99E-95 5.49E-94 -9.32157 -9.32157 -9.32157 -0.0733843 -0.3162863 -0.2790863 5 847.28604 9.7267053 1.49E-77 1.33E-76 -8.215888 -8.215888 -8.215888 0.631853 0.3966124 0.4940631 204 64000 6500306 memo 9.3744036 791.81993 9.6290286 8.59E-75 7.38E-74 -8.2711026 -8.2711026 -8.2711026 0.4262034 0.3831127 0.2707696 136.06836 EASDEES 726.06516 9.5039552 2.36E-69 1.87E-68 -6.8822306 -6.8822306 -6.8822306 1.5912286 1.7160924 1.5676387 600 4400302402006 4.36.363 ******* 2443603 **** 100*50*5.240*30 33103836 608.11897 9.2482098 1.2E-267 5.95E-266-7.9296227 -4.7142693 -7.9296227 2.9934394 3.2481759 3.2192825 www.c SERVEET MUO *600*65 0.0384336 0.000000 ***************** 456.80467 8.8354336 2.38E-43 -9.090888 -9.090888 -9.090888 -1.1241791 -1.4468333 -1.2171597 www.www 0:0934350 6104343 404247 076474 4064376* $0413500 C10423 384.39701 8.5864533 3.782E-39 1.792E-38 -9.5491347 -9.5491347 -9.5491347 -1.975471 -1.9613751 -1.9412599 www 367.82505 8.5228759 2.41E-37 11367.62505 6.5226159 ZNIES! 346.01397 8.4346865 1.09E-117 340.01997 0340009 4.56E-44 12 13 299.68622 8.2273089 4.24E-31 14 278.67084 8.1224182 3.13E-94 17 239.98475 7.9067989 4.70E-123 18 18 238.77865 1.10E-36 -8.6796094 -8.6796094 -8.6796094 -1.0796112 -1.2430199 -1.1466266 196094 -8.6796094 -1.0796112 -1.2430199 -1.1466266 BUCO HO 1.53E-116 -6.2563842 -8.8207137 -8.8207137 0.5240714 0.6412797 0.7507498 1.53E-110 -6.2563642 -6.8207137 -8.8207137 0.5240714 0.6412797 0.7507498 1.66E-30 -8.3760452 -8.3760452 -8.3760452 -1.1290682 -1.181848 -1.125163 -1.101646 -1.125163 3.41E-93-6.5188956 -6.5188956 -3.9634506 2.7864228 2.5182696 2.5766006 15 277.74252 8.1176043 1.11E-252 4.89E-251 -4.824966 -5.8989967 -5.7064293 2.602651 2.6864677 2.481924 16 10 259.38227 8.0189361 1.16E-26 4.07E-26 -8.4181912 -8.4181912 -8.4181912 -1.4660267 -1.5624062 -1.1988073 6.92E-122 -8.0754611 -4.8601077 -8.0754611 1.840504 1.6763788 1.4771684 -2.578528 1.86E-24 -6.424638 0.3993354 0.5234777 -6.424638 -6.424638 0475226 0.475236 6.0519258 1260692 04505629 02011205 2.06E-76 -8.6073708 -8.6073708 -6.0519258 0.1260692 0.4506639 0.2011305 3.26E-23 -9.1944906 -9.1944906 -9.1944906 -2.326509 -2.5992509 -2.21725 9.24E-133 -8.5795786 -8.5795786 -5.1523782 1.0913564 1.0728451 0.9667178 2.43E-22 -5.4410844 -5.4410844 -5.4410844 1.382889 1.035158 1.5361562 1.49E-21 -8.2515508 -8.2515508 -8.2515508 -1.1444625 -1.5463855 -1.8165229 2.19E-22 -9.8659117 -9.8659117 -9.8659117 -3.0419383 -3.0586068 -3.2266579 7.89953 19 236.26536 7.8842643 4485-24-9 5176038 -9 5176038 -9 5176038 -2.8844576 -2.4008619 20 330 12216 229.13316 7 8400424 1.36E-24 5.56E-25 7.8400424 2.31E-77 226.52461 7.823524 1.01E-23 220.17798 7.7825264 5.61E-134 219.35572 7.7771285 7.71E-23 21 22 22 23 24 217.6387 7.7657913 4.81E-22 25 215.16056 7.7492699 6.93E-23 DE_analysis + < H > K FDR R I 0 0 0 0 0 = 0 = 0 9 0 9 0 9 1 2 0 9 0 0 2 2 0 0 0 O 0 O 0 0 0 0 0 0 0 0 ◄ 0 0 0 0 0 = 2 • 0 9 0 9 0 9 0 9 0 0 0 1 + 0 2 0 0 O 0 0 0 0 0 O 0 0 0 0 0 0 0 = 0 0 = 0 9 0 9 0 9 0 9 0 0 1 ↓ 1 0 0 0 0 0 1 1 O 0 2 2 0 0 0 500 173 131 118 *** 101 553 71 54 55 185 43 180 531 35 275 28 32 121 33 232 32 39 32 475 134 102 105 101 *v* 605 52 50 45 43 184 38 137 516 30 225 36 32 139 25 210 23 27 29 557 160 127 113 106 690 71 2 59 34 56 30 231 46 166 521 45 228 37 36 36 136 38 227 38 26 30
Biology Today and Tomorrow without Physiology (MindTap Course List)
5th Edition
ISBN:9781305117396
Author:Cecie Starr, Christine Evers, Lisa Starr
Publisher:Cecie Starr, Christine Evers, Lisa Starr
Chapter10: Biotechnology
Section: Chapter Questions
Problem 4DID
Related questions
Concept explainers
Genetic Variation
Genetic variation refers to the variation in the genome sequences between individual organisms of a species. Individual differences or population differences can both be referred to as genetic variations. It is primarily caused by mutation, but other factors such as genetic drift and sexual reproduction also play a major role.
Quantitative Genetics
Quantitative genetics is the part of genetics that deals with the continuous trait, where the expression of various genes influences the phenotypes. Thus genes are expressed together to produce a trait with continuous variability. This is unlike the classical traits or qualitative traits, where each trait is controlled by the expression of a single or very few genes to produce a discontinuous variation.
Question
the topic is Identification of Differentially Expressed Genes in Breast Cancer Using RNA-Seq
write a method section of a scientific report for this topic.
including the use of excel to get these result( will be included in the images) and also this website https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216238
Transcribed Image Text:T
U
Raw counts
1
2 foldchange log2FC
3 3604.4176 11.81555 2.85E-284
557
160
127
113
106
8 608.11897 9.2482098 1.2E-267
690
71
59
56
231
46
166
KTB_103_pr KTB103_prir KTB103_prir KTB_103_TC KTB_103_TC KTB_103_TCKTB_103_pr KTB103_prir KTB103_prir KTB_103_TC KTB_103_TC KTB_103_TONSL-F_S22
1.55E-282 -9.3129082 -9.3129082 -9.3129082 1.4648813 1.5160533 1.5272297
4 1099.1348 10.102153 4.99E-95 5.49E-94 -9.32157 -9.32157 -9.32157 -0.0733843 -0.3162863 -0.2790863
5 847.28604 9.7267053 1.49E-77 1.33E-76 -8.215888 -8.215888 -8.215888 0.631853 0.3966124 0.4940631
6 791.81993 9.6290286 8.59E-75 7.38E-74 -8.2711026 -8.2711026 -8.2711026 0.4262034 0.3831127 0.2707696
7 726.06516 9.5039552 2.36E-69 1.87E-68 -6.8822306 -6.8822306 -6.8822306 1.5912286 1.7160924 1.5676387
-4.7142693 -7.9296227 2.9934394 3.2481759 3.2192825
9 456.80467 8.8354336 4.56E-44 2.38E-43 -9.090888 -9.090888 -9.090888 -1.1241791 -1.4468333 -1.2171597
10 384.39701 8.5864533 3.782E-39 1.792E-38 -9.5491347 -9.5491347 -9.5491347 -1.975471 -1.9613751 -1.9412599
11 367.82505 8.5228759 2.41E-37 1.10E-36 -8.6796094 -8.6796094 -8.6796094 -1.0796112 -1.2430199 -1.1466266
12 346.01397 8.4346865 1.09E-117 1.53E-116 -6.2563842 -8.8207137 -8.8207137 0.5240714 0.6412797 0.7507498
13 299.68622 8.2273089 4.24E-31 1.66E-30 -8.3760452 -8.3760452 -8.3760452 -1.1290682 -1.181848 -1.125163
14 278.67084 8.1224182 3.13E-94 3.41E-93 -6.5188956 -6.5188956 -3.9634506 2.7864228 2.5182696 2.5766006
15 277.74252 8.1176043 1.11E-252 4.89E-251 -4.824966 -5.8989967 -5.7064293 2.602651 2.6864677 2.481924
16 259.38227 8.0189361 1.16E-26 4.07E-26 -8.4181912 -8.4181912 -8.4181912 -1.4660267 -1.5624062 -1.1988073
17 239.98475 7.9067989 4.70E-123 6.92E-122 -8.0754611 -4.8601077 -8.0754611 1.840504 1.6763788 1.4771684
18 238.77865 7.89953 1.36E-24 4.48E-24 -9.5176038 -9.5176038 -9.5176038 -2.8844576 -2.4008619 -2.578528
19 236.26536 7.8842643 5.56E-25 1.86E-24 -6.424638 -6.424638 -6.424638 0.3993354 0.5234777 0.475236
20 229.13316 7.8400424 2.31E-77 2.06E-76 -8.6073708 -8.6073708 -6.0519258 0.1260692 0.4506639 0.2011305
21 226.52461 7.823524 1.01E-23 3.26E-23 -9.1944906 -9.1944906 -9.1944906 -2.326509 -2.5992509 -2.21725
22 220.17798 7.7825264 5.61E-134 9.24E-133 -8.5795786 -8.5795786 -5.1523782 1.0913564 1.0728451 0.9667178
23 219.35572 7.7771285 7.71E-23 2.43E-22 -5.4410844 -5.4410844 -5.4410844 1.382889 1.035158 1.5361562
24 217.6387 7.7657913 4.81E-22
1.49E-21 -8.2515508 -8.2515508 -8.2515508 -1.1444625 -1.5463855 -1.8165229
25 215.16056 7.7492699 6.93E-23 2.19E-22 -9.8659117 -9.8659117 -9.8659117 -3.0419383 -3.0586068 -3.2266579
+
521
45
228
37
36
136
38
227
38
26
30
DE analysis
>
H
TUPE
J
TONSL vs Primary
PValue
FDR
K
L
5.95E-266-7.9296227
M
N
log2FPKM
P
Q
R
A
0
0
0
0
0
0
0
0
0
1
0
0
2
0
0
0
0
0
0
0
0
0
0
◄
S
0
0
0
0
0
2
0
0
0
0
0
0
1
0
2
0
0
bo o o o o o
0
0
0
0
0
0
0
0
0
0
0
0
0
1
1
0
0
0
0
1
0
2
0
0
0
500
173
131
118
101
553
71
54
55
185
43
180
531
35
275
28
32
121
33
232
32
39
32
V
475
134
102
105
101
605
52
50
45
184
38
137
516
30
225
36
32
139
25
210
23
27
29
B
Ia
W
m
X
Y
Transcribed Image Text:A
1
2 GeneSymbo Chr
3 EYA4
4 GALNT13
B
24 GABRA3
25 NCAM1
Start
C
DE analysis
D
Gene information
End
chr6;chr6;ch 133241357;1133241749;1+;+;+;+;+;+;+
chr2;chr2;ch 153871898;1153872303;1+;+;+;+;+;+;+
chr5;chr5;ch 51383124;5151383699;51+;+;+;+;+;+
chr6;chr6;ch 33721666;3333723187;33-
5 ISL1
6 IP6K3
8 PINCR
7 ZFPM2-AS1 chr8;chr8;ch 105780410;1105780567;1-;-;-
chrX;chrX;ch 43176994;4343177205;43 +;+;+;+;+;+
chr1;chr1;ch 39678648;3939682733;39-
chr12;chr12; 111034024;1111034240;1+;+;+;+;+
chr8;chr8;ch 19939071;19 19939528; 19+;+;+;+;+
chr20;chr20; 62708837;6262709921;62+;+;+;+
chr17;chr17 48724765;4848727043;4 -;-
chr8;chr8;ch 81478497;8181478915;81-;-;-;-
chr7;chr7;ch 28995231;28 28995882;28 -;-
9 HPCAL4
10 CUX2
11 LPL
12 NTSR1
13 HOXB13
14 FABP4
15 CPVL
16 LOC1004205 chr19;chr19; 28435389;28 28436815;28-;-;-;-;
17 SAMSN1 chr21;chr21; 14485228;1414486114;14-;-;-
18 LOC642366 chr5;chr5 51372737;5151379075;51-;-
19 CSF2
chr5;chr5;ch 132073792;1132073982;1+;+;+;+
chr4;chr4;ch 166733385;1166735090;1-
chr2;chr2;ch 26848101;2€ 26848254;2(+;+;+;+;+
chr18;chr18; 32937402;3232938091;31-;-;-;-
chr16;chr16; 56638666;5(56638766;5(+;+;+
chrx;chrX;ch 152167162;1152168563;1-
20 SPOCK3
21 DPYSL5
22 CCDC178
23 MT1A
E
Strand
chr11;chr11;112961247; 112961664; +;
J
TONSL vs Primary
log2FPKM
Length Description foldchange log2FC PValue
KTB 103 pr KTB103 prir KTB103 prir KTB 103 TC KTB 103 TC KTB 103 TQKTB 103
5812 EYA transcri 3604.4176 11.81555 2.85E-284 1.55E-282 -9.3129082 -9.3129082 -9.3129082 1.4648813 1.5160533 1.5272297
5847 polypeptide 1099.1348 10.102153 4.99E-95 5.49E-94 -9.32157 -9.32157 -9.32157 -0.0733843 -0.3162863 -0.2790863
2717 ISL LIM hom 847.28604 9.7267053 1.49E-77 1.33E-76 -8.215888 -8.215888 -8.215888 0.631853 0.3966124 0.4940631
2823 inositol hex 791.81993 9.6290286 8.59E-75 7.38E-74 -8.2711026 -8.2711026 -8.2711026 0.4262034 0.3831127 0.2707696
1078 ZFPM2 antis 726.06516 9.5039552 2.36E-69 1.87E-68 -6.8822306 -6.8822306 -6.8822306 1.5912286 1.7160924 1.5676387
2228 p53-induced 608.11897 9.2482098 1.2E-267 5.95E-266 -7.9296227 -4.7142693 -7.9296227 2.9934394 3.2481759 3.2192825
4983 hippocalcin 456.80467 8.8354336 4.56E-44 2.38E-43 -9.090888 -9.090888 -9.090888 -1.1241791 -1.4468333 -1.2171597
6846 cut like hom 384.39701 8.5864533 3.782E-39 1.792E-38 -9.5491347 -9.5491347 -9.5491347 -1.975471 -1.9613751 -1.9412599
3747 lipoprotein 367.82505 8.5228759 2.41E-37 1.10E-36 -8.6796094 -8.6796094 -8.6796094 -1.0796112 -1.2430199 -1.1466266
4132 neurotensin 346.01397 8.4346865 1.09E-117 1.53E-116 -6.2563842 -8.8207137 -8.8207137 0.5240714 0.6412797 0.7507498
3036 homeobox 299.68622 8.2273089 4.24E-31 1.66E-30 -8.3760452 -8.3760452 -8.3760452 -1.1290682 -1.181848 -1.125163
838 fatty acid bi 278.67084 8.1224182 3.13E-94 3.41E-93 -6.5188956 -6.5188956 -3.9634506 2.7864228 2.5182696 2.5766006
2805 carboxypep 277.74252 8.1176043 1.11E-252 4.89E-251 -4.824966 -5.8989967 -5.7064293 2.602651 2.6864677 2.481924
3126 SHC binding 259.38227 8.0189361 1.16E-26 4.07E-26 -8.4181912 -8.4181912 -8.4181912 -1.4660267 -1.5624062 -1.1988073
2465 SAM domair 239.98475 7.9067989 4.70E-123 6.92E-122 -8.0754611 -4.8601077 -8.0754611 1.840504 1.6763788 1.4771684
6698 uncharacter 238.77865 7.89953 1.36E-24 4.48E-24 -9.5176038 -9.5176038 -9.5176038 -2.8844576 -2.4008619 -2.578528
785 colony stim 236.26536 7.8842643 5.56E-25 1.86E-24 -6.424638 -6.424638 -6.424638 0.3993354 0.5234777 0.475236
3564 SPARC (oste 229.13316 7.8400424 2.31E-77 2.06E-76 -8.6073708 -8.6073708 -6.0519258 0.1260692 0.4506639 0.2011305
5354 dihydropyri 226.52461 7.823524 1.01E-23 3.26E-23 -9.1944906 -9.1944906 -9.1944906 -2.326509 -2.5992509 -2.21725
3496 coiled-coil d 220.17798 7.7825264 5.61E-134 9.24E-133 -8.5795786 -8.5795786 -5.1523782 1.0913564 1.0728451 0.9667178
397 metallothio 219.35572 7.7771285 7.71E-23 2.43E-22 -5.4410844 -5.4410844 -5.4410844 1.382889 1.035158 1.5361562
2785 gamma-ami 217.6387 7.7657913 4.81E-22 1.49E-21 -8.2515508 -8.2515508 -8.2515508 -1.1444625 -1.5463855 -1.8165229
8527 neural cell a 215.16056 7.7492699 6.93E-23 2.19E-22 -9.8659117 -9.8659117 -9.8659117 -3.0419383 -3.0586068 -3.2266579
F
G
H
FDR
K
L
M
N
P
Q
R
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