-
1
-
-
33750412872
-
Surviving cell death through epidermal growth factor (EGF) signal transduction pathways: implications for cancer therapy
-
10.1016/j.cellsig.2006.05.015, 16815674
-
Henson ES, Gibson SB. Surviving cell death through epidermal growth factor (EGF) signal transduction pathways: implications for cancer therapy. Cell Signal 2006, 18(12):2089-2097. 10.1016/j.cellsig.2006.05.015, 16815674.
-
(2006)
Cell Signal
, vol.18
, Issue.12
, pp. 2089-2097
-
-
Henson, E.S.1
Gibson, S.B.2
-
2
-
-
10744230127
-
An open-and-shut case? Recent insights into the activation of EGF/ErbB receptors
-
10.1016/S1097-2765(03)00350-2, 14527402
-
Burgess AW, Cho HS, Eigenbrot C, Ferguson KM, Garrett TP, Leahy DJ, Lemmon MA, Sliwkowski MX, Ward CW, Yokoyama S. An open-and-shut case? Recent insights into the activation of EGF/ErbB receptors. Mol Cell 2003, 12(3):541-552. 10.1016/S1097-2765(03)00350-2, 14527402.
-
(2003)
Mol Cell
, vol.12
, Issue.3
, pp. 541-552
-
-
Burgess, A.W.1
Cho, H.S.2
Eigenbrot, C.3
Ferguson, K.M.4
Garrett, T.P.5
Leahy, D.J.6
Lemmon, M.A.7
Sliwkowski, M.X.8
Ward, C.W.9
Yokoyama, S.10
-
3
-
-
0037211253
-
Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs): simple drugs with a complex mechanism of action?
-
10.1002/jcp.10194, 12447985
-
Normanno N, Maiello MR, De Luca A. Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs): simple drugs with a complex mechanism of action?. J Cell Physiol 2003, 194:13-19. 10.1002/jcp.10194, 12447985.
-
(2003)
J Cell Physiol
, vol.194
, pp. 13-19
-
-
Normanno, N.1
Maiello, M.R.2
De Luca, A.3
-
4
-
-
77953850680
-
EGF decreases the abundance of microRNAs that restrain oncogenic transcription factors
-
10.1126/scisignal.2000876, 20516477
-
Avraham R, Sas-Chen A, Manor O, Steinfeld I, Shalgi R, Tarcic G, Bossel N, Zeisel A, Amit I, Zwang Y, Enerly E, Russnes HG, Biagioni F, Mottolese M, Strano S, Blandino G, Borresen-Dale AL, Pilpel Y, Yakhini Z, Segal E, Yarden Y. EGF decreases the abundance of microRNAs that restrain oncogenic transcription factors. Sci Signal 2010, 3(124):ra43. 10.1126/scisignal.2000876, 20516477.
-
(2010)
Sci Signal
, vol.3
, Issue.124
-
-
Avraham, R.1
Sas-Chen, A.2
Manor, O.3
Steinfeld, I.4
Shalgi, R.5
Tarcic, G.6
Bossel, N.7
Zeisel, A.8
Amit, I.9
Zwang, Y.10
Enerly, E.11
Russnes, H.G.12
Biagioni, F.13
Mottolese, M.14
Strano, S.15
Blandino, G.16
Borresen-Dale, A.L.17
Pilpel, Y.18
Yakhini, Z.19
Segal, E.20
Yarden, Y.21
more..
-
5
-
-
33645730357
-
Activation of mitogen-activated protein kinase in estrogen receptor alpha-positive breast cancer cells in vitro induces an in vivo molecular phenotype of estrogen receptor alpha-negative human breast tumors
-
10.1158/0008-5472.CAN-05-4363, 16585219
-
Creighton CJ, Hilger AM, Murthy S, Rae JM, Chinnaiyan AM, El-Ashry D. Activation of mitogen-activated protein kinase in estrogen receptor alpha-positive breast cancer cells in vitro induces an in vivo molecular phenotype of estrogen receptor alpha-negative human breast tumors. Cancer Res 2006, 66(7):3903-3911. 10.1158/0008-5472.CAN-05-4363, 16585219.
-
(2006)
Cancer Res
, vol.66
, Issue.7
, pp. 3903-3911
-
-
Creighton, C.J.1
Hilger, A.M.2
Murthy, S.3
Rae, J.M.4
Chinnaiyan, A.M.5
El-Ashry, D.6
-
6
-
-
33746068303
-
Epidermal growth factor receptor activation: an upstream signal for transition of quiescent astrocytes into reactive astrocytes after neural injury
-
10.1523/JNEUROSCI.1004-06.2006, 16837601
-
Liu B, Chen H, Johns TG, Neufeld AH. Epidermal growth factor receptor activation: an upstream signal for transition of quiescent astrocytes into reactive astrocytes after neural injury. J Neurosci 2006, 26(28):7532-7540. 10.1523/JNEUROSCI.1004-06.2006, 16837601.
-
(2006)
J Neurosci
, vol.26
, Issue.28
, pp. 7532-7540
-
-
Liu, B.1
Chen, H.2
Johns, T.G.3
Neufeld, A.H.4
-
7
-
-
23044432130
-
Microarray analysis of early adipogenesis in C3H10T1/2 cells: cooperative inhibitory effects of growth factors and 2,3,7,8-tetrachlorodibenzo-p-dioxin
-
10.1016/j.taap.2004.12.004, 16054899
-
Hanlon PR, Cimafranca MA, Liu X, Cho YC, Jefcoate CR. Microarray analysis of early adipogenesis in C3H10T1/2 cells: cooperative inhibitory effects of growth factors and 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicol Appl Pharmacol 2005, 207(1):39-58. 10.1016/j.taap.2004.12.004, 16054899.
-
(2005)
Toxicol Appl Pharmacol
, vol.207
, Issue.1
, pp. 39-58
-
-
Hanlon, P.R.1
Cimafranca, M.A.2
Liu, X.3
Cho, Y.C.4
Jefcoate, C.R.5
-
8
-
-
51349159152
-
Displayed correlation between gene expression profiles and submicroscopic alterations in response to cetuximab, gefitinib and EGF in human colon cancer cell lines
-
10.1186/1471-2407-8-227, 2528013, 18691415
-
Solmi R, Lauriola M, Francesconi M, Martini D, Voltattorni M, Ceccarelli C, Ugolini G, Rosati G, Zanotti S, Montroni I, Mattei G, Taffurelli M, Santini D, Pezzetti F, Ruggeri A, Castellani G, Guidotti L, Coppola D, Strippoli P. Displayed correlation between gene expression profiles and submicroscopic alterations in response to cetuximab, gefitinib and EGF in human colon cancer cell lines. BMC Cancer 2008, 8:227. 10.1186/1471-2407-8-227, 2528013, 18691415.
-
(2008)
BMC Cancer
, vol.8
, pp. 227
-
-
Solmi, R.1
Lauriola, M.2
Francesconi, M.3
Martini, D.4
Voltattorni, M.5
Ceccarelli, C.6
Ugolini, G.7
Rosati, G.8
Zanotti, S.9
Montroni, I.10
Mattei, G.11
Taffurelli, M.12
Santini, D.13
Pezzetti, F.14
Ruggeri, A.15
Castellani, G.16
Guidotti, L.17
Coppola, D.18
Strippoli, P.19
-
9
-
-
33745084520
-
PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli
-
10.1186/gb-2006-7-5-r42, 1779520, 16737555
-
Gu J, Iyer VR. PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli. Genome Biol 2006, 7(5):R42. 10.1186/gb-2006-7-5-r42, 1779520, 16737555.
-
(2006)
Genome Biol
, vol.7
, Issue.5
-
-
Gu, J.1
Iyer, V.R.2
-
10
-
-
33947547741
-
Quantitative transcriptional control of ErbB receptor signaling undergoes graded to biphasic response for cell differentiation
-
Nagashima T, Shimodaira H, Ide K, Nakakuki T, Tani Y, Takahashi K, Yumoto N, Hatakeyama M. Quantitative transcriptional control of ErbB receptor signaling undergoes graded to biphasic response for cell differentiation. J Biol Chem 2007, 282(6):4045-4056.
-
(2007)
J Biol Chem
, vol.282
, Issue.6
, pp. 4045-4056
-
-
Nagashima, T.1
Shimodaira, H.2
Ide, K.3
Nakakuki, T.4
Tani, Y.5
Takahashi, K.6
Yumoto, N.7
Hatakeyama, M.8
-
11
-
-
34047174559
-
A module of negative feedback regulators defines growth factor signaling
-
10.1038/ng1987, 17322878
-
Amit I, Citri A, Shay T, Lu Y, Katz M, Zhang F, Tarcic G, Siwak D, Lahad J, Jacob-Hirsch J, Amariglio N, Vaisman N, Segal E, Rechavi G, Alon U, Mills GB, Domany E, Yarden Y. A module of negative feedback regulators defines growth factor signaling. Nat Genet 2007, 39(4):503-512. 10.1038/ng1987, 17322878.
-
(2007)
Nat Genet
, vol.39
, Issue.4
, pp. 503-512
-
-
Amit, I.1
Citri, A.2
Shay, T.3
Lu, Y.4
Katz, M.5
Zhang, F.6
Tarcic, G.7
Siwak, D.8
Lahad, J.9
Jacob-Hirsch, J.10
Amariglio, N.11
Vaisman, N.12
Segal, E.13
Rechavi, G.14
Alon, U.15
Mills, G.B.16
Domany, E.17
Yarden, Y.18
-
12
-
-
77951963192
-
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data
-
10.1186/1471-2105-11-232, 2875242, 20459641
-
Imamura H, Yachie N, Saito R, Ishihama Y, Tomita M. Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. BMC Bioinformatics 2010, 11:232. 10.1186/1471-2105-11-232, 2875242, 20459641.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 232
-
-
Imamura, H.1
Yachie, N.2
Saito, R.3
Ishihama, Y.4
Tomita, M.5
-
13
-
-
77952017101
-
Quantitative analysis of HGF and EGF-dependent phosphotyrosine signaling networks
-
10.1021/pr100145w, 20222723
-
Hammond DE, Hyde R, Kratchmarova I, Beynon RJ, Blagoev B, Clague MJ. Quantitative analysis of HGF and EGF-dependent phosphotyrosine signaling networks. J Proteome Res 2010, 9(5):2734-2742. 10.1021/pr100145w, 20222723.
-
(2010)
J Proteome Res
, vol.9
, Issue.5
, pp. 2734-2742
-
-
Hammond, D.E.1
Hyde, R.2
Kratchmarova, I.3
Beynon, R.J.4
Blagoev, B.5
Clague, M.J.6
-
14
-
-
33750456519
-
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
-
10.1016/j.cell.2006.09.026, 17081983
-
Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127(3):635-648. 10.1016/j.cell.2006.09.026, 17081983.
-
(2006)
Cell
, vol.127
, Issue.3
, pp. 635-648
-
-
Olsen, J.V.1
Blagoev, B.2
Gnad, F.3
Macek, B.4
Kumar, C.5
Mortensen, P.6
Mann, M.7
-
15
-
-
0035233239
-
Genomic-scale measurement of mRNA turnover and the mechanisms of action of the anti-cancer drug flavopiridol
-
57796, 11597333
-
Lam LT, Pickeral OK, Peng AC, Rosenwald A, Hurt EM, Giltnane JM, Averett LM, Zhao H, Davis RE, Sathyamoorthy M, Wahl LM, Harris ED, Mikovits JA, Monks AP, Hollingshead MG, Sausville EA, Staudt LM. Genomic-scale measurement of mRNA turnover and the mechanisms of action of the anti-cancer drug flavopiridol. Genome Biol 2001, 2(10):RESEARCH0041. 57796, 11597333.
-
(2001)
Genome Biol
, vol.2
, Issue.10
-
-
Lam, L.T.1
Pickeral, O.K.2
Peng, A.C.3
Rosenwald, A.4
Hurt, E.M.5
Giltnane, J.M.6
Averett, L.M.7
Zhao, H.8
Davis, R.E.9
Sathyamoorthy, M.10
Wahl, L.M.11
Harris, E.D.12
Mikovits, J.A.13
Monks, A.P.14
Hollingshead, M.G.15
Sausville, E.A.16
Staudt, L.M.17
-
16
-
-
4444263072
-
Transcriptional signature of flavopiridol-induced tumor cell death
-
Lu X, Burgan WE, Cerra MA, Chuang EY, Tsai MH, Tofilon PJ, Camphausen K. Transcriptional signature of flavopiridol-induced tumor cell death. Mol Cancer Ther 2004, 3(7):861-872.
-
(2004)
Mol Cancer Ther
, vol.3
, Issue.7
, pp. 861-872
-
-
Lu, X.1
Burgan, W.E.2
Cerra, M.A.3
Chuang, E.Y.4
Tsai, M.H.5
Tofilon, P.J.6
Camphausen, K.7
-
17
-
-
15944415822
-
Chemosensitivity profile of cancer cell lines and identification of genes determining chemosensitivity by an integrated bioinformatical approach using cDNA arrays
-
Nakatsu N, Yoshida Y, Yamazaki K, Nakamura T, Dan S, Fukui Y, Yamori T. Chemosensitivity profile of cancer cell lines and identification of genes determining chemosensitivity by an integrated bioinformatical approach using cDNA arrays. Mol Cancer Ther 2005, 4(3):399-412.
-
(2005)
Mol Cancer Ther
, vol.4
, Issue.3
, pp. 399-412
-
-
Nakatsu, N.1
Yoshida, Y.2
Yamazaki, K.3
Nakamura, T.4
Dan, S.5
Fukui, Y.6
Yamori, T.7
-
18
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
10.1126/science.1081900, 12843395
-
Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 2003, 301(5629):102-105. 10.1126/science.1081900, 12843395.
-
(2003)
Science
, vol.301
, Issue.5629
, pp. 102-105
-
-
Gardner, T.S.1
di Bernardo, D.2
Lorenz, D.3
Collins, J.J.4
-
19
-
-
48549086654
-
Cross-platform comparison of SYBR Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study
-
10.1186/1471-2164-9-328, 2491643, 18620571
-
Arikawa E, Sun Y, Wang J, Zhou Q, Ning B, Dial SL, Guo L, Yang J. Cross-platform comparison of SYBR Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study. BMC Genomics 2008, 9:328. 10.1186/1471-2164-9-328, 2491643, 18620571.
-
(2008)
BMC Genomics
, vol.9
, pp. 328
-
-
Arikawa, E.1
Sun, Y.2
Wang, J.3
Zhou, Q.4
Ning, B.5
Dial, S.L.6
Guo, L.7
Yang, J.8
-
20
-
-
33748503420
-
Evaluation of DNA microarray results with quantitative gene expression platforms
-
10.1038/nbt1236, 16964225
-
Canales RD, Luo Y, Willey JC, Austermiller B, Barbacioru CC, Boysen C, Hunkapiller K, Jensen RV, Knight CR, Lee KY, Ma Y, Maqsodi B, Papallo A, Peters EH, Poulter K, Ruppel PL, Samaha RR, Shi L, Yang W, Zhang L, Goodsaid FM. Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol 2006, 24(9):1115-1122. 10.1038/nbt1236, 16964225.
-
(2006)
Nat Biotechnol
, vol.24
, Issue.9
, pp. 1115-1122
-
-
Canales, R.D.1
Luo, Y.2
Willey, J.C.3
Austermiller, B.4
Barbacioru, C.C.5
Boysen, C.6
Hunkapiller, K.7
Jensen, R.V.8
Knight, C.R.9
Lee, K.Y.10
Ma, Y.11
Maqsodi, B.12
Papallo, A.13
Peters, E.H.14
Poulter, K.15
Ruppel, P.L.16
Samaha, R.R.17
Shi, L.18
Yang, W.19
Zhang, L.20
Goodsaid, F.M.21
more..
-
21
-
-
0141905890
-
Evaluation of gene expression measurements from commercial microarray platforms
-
10.1093/nar/gkg763, 206463, 14500831
-
Tan PK, Downey TJ, Spitznagel EL, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 2003, 31(19):5676-5684. 10.1093/nar/gkg763, 206463, 14500831.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.19
, pp. 5676-5684
-
-
Tan, P.K.1
Downey, T.J.2
Spitznagel, E.L.3
Xu, P.4
Fu, D.5
Dimitrov, D.S.6
Lempicki, R.A.7
Raaka, B.M.8
Cam, M.C.9
-
22
-
-
33645808222
-
Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays
-
10.1186/1471-2164-7-59, 1435885, 16551369
-
Wang Y, Barbacioru C, Hyland F, Xiao W, Hunkapiller KL, Blake J, Chan F, Gonzalez C, Zhang L, Samaha RR. Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays. BMC Genomics 2006, 7:59. 10.1186/1471-2164-7-59, 1435885, 16551369.
-
(2006)
BMC Genomics
, vol.7
, pp. 59
-
-
Wang, Y.1
Barbacioru, C.2
Hyland, F.3
Xiao, W.4
Hunkapiller, K.L.5
Blake, J.6
Chan, F.7
Gonzalez, C.8
Zhang, L.9
Samaha, R.R.10
-
23
-
-
7744245590
-
Comparison of microarray-based mRNA profiling technologies for identification of psychiatric disease and drug signatures
-
10.1016/j.jneumeth.2004.04.002, 15325126
-
Jurata LW, Bukhman YV, Charles V, Capriglione F, Bullard J, Lemire AL, Mohammed A, Pham Q, Laeng P, Brockman JA, Altar CA. Comparison of microarray-based mRNA profiling technologies for identification of psychiatric disease and drug signatures. J Neurosci Methods 2004, 138(1-2):173-188. 10.1016/j.jneumeth.2004.04.002, 15325126.
-
(2004)
J Neurosci Methods
, vol.138
, Issue.1-2
, pp. 173-188
-
-
Jurata, L.W.1
Bukhman, Y.V.2
Charles, V.3
Capriglione, F.4
Bullard, J.5
Lemire, A.L.6
Mohammed, A.7
Pham, Q.8
Laeng, P.9
Brockman, J.A.10
Altar, C.A.11
-
24
-
-
48949120304
-
Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells
-
10.1186/1471-2164-9-302, 2464609, 18578872
-
Maouche S, Poirier O, Godefroy T, Olaso R, Gut I, Collet JP, Montalescot G, Cambien F. Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells. BMC Genomics 2008, 9:302. 10.1186/1471-2164-9-302, 2464609, 18578872.
-
(2008)
BMC Genomics
, vol.9
, pp. 302
-
-
Maouche, S.1
Poirier, O.2
Godefroy, T.3
Olaso, R.4
Gut, I.5
Collet, J.P.6
Montalescot, G.7
Cambien, F.8
-
25
-
-
34248183381
-
Cross platform microarray analysis for robust identification of differentially expressed genes
-
10.1186/1471-2105-8-S1-S5, 2230506, 18269699
-
Bosotti R, Locatelli G, Healy S, Scacheri E, Sartori L, Mercurio C, Calogero R, Isacchi A. Cross platform microarray analysis for robust identification of differentially expressed genes. BMC Bioinformatics 2007, 8(Suppl 1):S5. 10.1186/1471-2105-8-S1-S5, 2230506, 18269699.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 1
-
-
Bosotti, R.1
Locatelli, G.2
Healy, S.3
Scacheri, E.4
Sartori, L.5
Mercurio, C.6
Calogero, R.7
Isacchi, A.8
-
26
-
-
42649121626
-
Can subtle changes in gene expression be consistently detected with different microarray platforms?
-
10.1186/1471-2164-9-124, 2335120, 18331641
-
Pedotti P, 't Hoen PA, Vreugdenhil E, Schenk GJ, Vossen RH, Ariyurek Y, de Hollander M, Kuiper R, van Ommen GJ, den Dunnen JT, Boer JM, de Menezes RX. Can subtle changes in gene expression be consistently detected with different microarray platforms?. BMC Genomics 2008, 9:124. 10.1186/1471-2164-9-124, 2335120, 18331641.
-
(2008)
BMC Genomics
, vol.9
, pp. 124
-
-
Pedotti, P.1
't Hoen, P.A.2
Vreugdenhil, E.3
Schenk, G.J.4
Vossen, R.H.5
Ariyurek, Y.6
de Hollander, M.7
Kuiper, R.8
van Ommen, G.J.9
den Dunnen, J.T.10
Boer, J.M.11
de Menezes, R.X.12
-
27
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
10.1126/science.1158441, 2951732, 18451266
-
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320(5881):1344-1349. 10.1126/science.1158441, 2951732, 18451266.
-
(2008)
Science
, vol.320
, Issue.5881
, pp. 1344-1349
-
-
Nagalakshmi, U.1
Wang, Z.2
Waern, K.3
Shou, C.4
Raha, D.5
Gerstein, M.6
Snyder, M.7
-
28
-
-
50649089207
-
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
-
10.1101/gr.079558.108, 2527709, 18550803
-
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18(9):1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
-
(2008)
Genome Res
, vol.18
, Issue.9
, pp. 1509-1517
-
-
Marioni, J.C.1
Mason, C.E.2
Mane, S.M.3
Stephens, M.4
Gilad, Y.5
-
29
-
-
53549106933
-
A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome
-
10.1186/1471-2164-9-418, 2562395, 18796152
-
Hanriot L, Keime C, Gay N, Faure C, Dossat C, Wincker P, Scote-Blachon C, Peyron C, Gandrillon O. A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome. BMC Genomics 2008, 9:418. 10.1186/1471-2164-9-418, 2562395, 18796152.
-
(2008)
BMC Genomics
, vol.9
, pp. 418
-
-
Hanriot, L.1
Keime, C.2
Gay, N.3
Faure, C.4
Dossat, C.5
Wincker, P.6
Scote-Blachon, C.7
Peyron, C.8
Gandrillon, O.9
-
30
-
-
57149085481
-
Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
-
2588528, 18927111
-
't Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, den Dunnen JT. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 2008, 36(28):e141. 2588528, 18927111.
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.28
-
-
't Hoen, P.A.1
Ariyurek, Y.2
Thygesen, H.H.3
Vreugdenhil, E.4
Vossen, R.H.5
de Menezes, R.X.6
Boer, J.M.7
van Ommen, G.J.8
den Dunnen, J.T.9
-
31
-
-
70349636603
-
Next-generation tag sequencing for cancer gene expression profiling
-
10.1101/gr.094482.109, 2765282, 19541910
-
Morrissy AS, Morin RD, Delaney A, Zeng T, McDonald H, Jones SJ, Zhao Y, Hirst M, Marra MA. Next-generation tag sequencing for cancer gene expression profiling. Genome Res 2009, 19(10):1825-35. 10.1101/gr.094482.109, 2765282, 19541910.
-
(2009)
Genome Res
, vol.19
, Issue.10
, pp. 1825-1835
-
-
Morrissy, A.S.1
Morin, R.D.2
Delaney, A.3
Zeng, T.4
McDonald, H.5
Jones, S.J.6
Zhao, Y.7
Hirst, M.8
Marra, M.A.9
-
32
-
-
66349083834
-
Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays
-
10.1186/1471-2164-10-221, 2686739, 19435513
-
Bloom JS, Khan Z, Kruglyak L, Singh M, Caudy AA. Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC Genomics 2009, 10:221. 10.1186/1471-2164-10-221, 2686739, 19435513.
-
(2009)
BMC Genomics
, vol.10
, pp. 221
-
-
Bloom, J.S.1
Khan, Z.2
Kruglyak, L.3
Singh, M.4
Caudy, A.A.5
-
33
-
-
74049148179
-
3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer
-
10.1186/1471-2164-10-531, 2781828, 19917133
-
Asmann YW, Klee EW, Thompson EA, Perez EA, Middha S, Oberg AL, Therneau TM, Smith DI, Poland GA, Wieben ED, Kocher JP. 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. BMC Genomics 2009, 10:531. 10.1186/1471-2164-10-531, 2781828, 19917133.
-
(2009)
BMC Genomics
, vol.10
, pp. 531
-
-
Asmann, Y.W.1
Klee, E.W.2
Thompson, E.A.3
Perez, E.A.4
Middha, S.5
Oberg, A.L.6
Therneau, T.M.7
Smith, D.I.8
Poland, G.A.9
Wieben, E.D.10
Kocher, J.P.11
-
34
-
-
77649318621
-
Digital gene expression analysis of two life cycle stages of the human-infective parasite, Trypanosoma brucei gambiense reveals differentially expressed clusters of co-regulated genes
-
10.1186/1471-2164-11-124, 2837033, 20175885
-
Veitch NJ, Johnson PC, Trivedi U, Terry S, Wildridge D, MacLeod A. Digital gene expression analysis of two life cycle stages of the human-infective parasite, Trypanosoma brucei gambiense reveals differentially expressed clusters of co-regulated genes. BMC Genomics 2010, 11:124. 10.1186/1471-2164-11-124, 2837033, 20175885.
-
(2010)
BMC Genomics
, vol.11
, pp. 124
-
-
Veitch, N.J.1
Johnson, P.C.2
Trivedi, U.3
Terry, S.4
Wildridge, D.5
MacLeod, A.6
-
35
-
-
77951777930
-
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling
-
10.1186/1471-2164-11-282, 2877694, 20444259
-
Bradford JR, Hey Y, Yates T, Li Y, Pepper SD, Miller CJ. A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics 2010, 11:282. 10.1186/1471-2164-11-282, 2877694, 20444259.
-
(2010)
BMC Genomics
, vol.11
, pp. 282
-
-
Bradford, J.R.1
Hey, Y.2
Yates, T.3
Li, Y.4
Pepper, S.D.5
Miller, C.J.6
-
36
-
-
33845345622
-
A rapid method for microarray cross platform comparisons using gene expression signatures
-
10.1016/j.mcp.2006.07.004, 16982174
-
Cheadle C, Becker KG, Cho-Chung YS, Nesterova M, Watkins T, Wood W, Prabhu V, Barnes KC. A rapid method for microarray cross platform comparisons using gene expression signatures. Mol Cell Probes 2007, 21(1):35-46. 10.1016/j.mcp.2006.07.004, 16982174.
-
(2007)
Mol Cell Probes
, vol.21
, Issue.1
, pp. 35-46
-
-
Cheadle, C.1
Becker, K.G.2
Cho-Chung, Y.S.3
Nesterova, M.4
Watkins, T.5
Wood, W.6
Prabhu, V.7
Barnes, K.C.8
-
37
-
-
27344435774
-
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
-
10.1073/pnas.0506580102, 1239896, 16199517
-
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005, 102(43):15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.43
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
Mesirov, J.P.11
-
38
-
-
38849106351
-
A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments
-
10.1093/bioinformatics/btm620, 18204063
-
Hong F, Breitling R. A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics 2008, 24(3):374-382. 10.1093/bioinformatics/btm620, 18204063.
-
(2008)
Bioinformatics
, vol.24
, Issue.3
, pp. 374-382
-
-
Hong, F.1
Breitling, R.2
-
39
-
-
33751006151
-
RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis
-
10.1093/bioinformatics/btl476, 16982708
-
Hong F, Breitling R, McEntee CW, Wittner BS, Nemhauser JL, Chory J. RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics 2006, 22(22):2825-2827. 10.1093/bioinformatics/btl476, 16982708.
-
(2006)
Bioinformatics
, vol.22
, Issue.22
, pp. 2825-2827
-
-
Hong, F.1
Breitling, R.2
McEntee, C.W.3
Wittner, B.S.4
Nemhauser, J.L.5
Chory, J.6
-
40
-
-
18244384210
-
Multiple-laboratory comparison of microarray platforms
-
10.1038/nmeth756, 15846361
-
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W. Multiple-laboratory comparison of microarray platforms. Nat Methods 2005, 2(5):345-350. 10.1038/nmeth756, 15846361.
-
(2005)
Nat Methods
, vol.2
, Issue.5
, pp. 345-350
-
-
Irizarry, R.A.1
Warren, D.2
Spencer, F.3
Kim, I.F.4
Biswal, S.5
Frank, B.C.6
Gabrielson, E.7
Garcia, J.G.8
Geoghegan, J.9
Germino, G.10
Griffin, C.11
Hilmer, S.C.12
Hoffman, E.13
Jedlicka, A.E.14
Kawasaki, E.15
Martinez-Murillo, F.16
Morsberger, L.17
Lee, H.18
Petersen, D.19
Quackenbush, J.20
Scott, A.21
Wilson, M.22
Yang, Y.23
Ye, S.Q.24
Yu, W.25
more..
-
41
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
-
10.1038/nbt1239, 16964229
-
Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006, 24(9):1151-1161. 10.1038/nbt1239, 16964229.
-
(2006)
Nat Biotechnol
, vol.24
, Issue.9
, pp. 1151-1161
-
-
Shi, L.1
Reid, L.H.2
Jones, W.D.3
Shippy, R.4
Warrington, J.A.5
Baker, S.C.6
Collins, P.J.7
de Longueville, F.8
Kawasaki, E.S.9
Lee, K.Y.10
Luo, Y.11
Sun, Y.A.12
Willey, J.C.13
Setterquist, R.A.14
Fischer, G.M.15
Tong, W.16
Dragan, Y.P.17
Dix, D.J.18
Frueh, F.W.19
Goodsaid, F.M.20
Herman, D.21
Jensen, R.V.22
Johnson, C.D.23
Lobenhofer, E.K.24
Puri, R.K.25
Schrf, U.26
Thierry-Mieg, J.27
Wang, C.28
Wilson, M.29
Wolber, P.K.30
more..
-
42
-
-
67650394369
-
Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing
-
10.1186/1471-2164-10-264, 2707382, 19523228
-
Mane SP, Evans C, Cooper KL, Crasta OR, Folkerts O, Hutchison SK, Harkins TT, Thierry-Mieg D, Thierry-Mieg J, Jensen RV. Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing. BMC Genomics 2009, 10:264. 10.1186/1471-2164-10-264, 2707382, 19523228.
-
(2009)
BMC Genomics
, vol.10
, pp. 264
-
-
Mane, S.P.1
Evans, C.2
Cooper, K.L.3
Crasta, O.R.4
Folkerts, O.5
Hutchison, S.K.6
Harkins, T.T.7
Thierry-Mieg, D.8
Thierry-Mieg, J.9
Jensen, R.V.10
-
43
-
-
74549191284
-
Computational modeling of the EGFR network elucidates control mechanisms regulating signal dynamics
-
10.1186/1752-0509-3-118, 2807436, 20028552
-
Wang DY, Cardelli L, Phillips A, Piterman N, Fisher J. Computational modeling of the EGFR network elucidates control mechanisms regulating signal dynamics. BMC Syst Biol 2009, 3:118. 10.1186/1752-0509-3-118, 2807436, 20028552.
-
(2009)
BMC Syst Biol
, vol.3
, pp. 118
-
-
Wang, D.Y.1
Cardelli, L.2
Phillips, A.3
Piterman, N.4
Fisher, J.5
-
44
-
-
77957762129
-
Dynamic interaction networks in a hierarchically organized tissue
-
2990637, 20924352
-
Kirouac DC, Ito C, Csaszar E, Roch A, Yu M, Sykes EA, Bader GD, Zandstra PW. Dynamic interaction networks in a hierarchically organized tissue. Mol Syst Biol 2010, 6:417. 2990637, 20924352.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 417
-
-
Kirouac, D.C.1
Ito, C.2
Csaszar, E.3
Roch, A.4
Yu, M.5
Sykes, E.A.6
Bader, G.D.7
Zandstra, P.W.8
-
45
-
-
50949092459
-
Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality
-
10.1371/journal.pcbi.1000140, 2467474, 18670624
-
Zotenko E, Mestre J, O'Leary DP, Przytycka TM. Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol 2008, 4(8):e1000140. 10.1371/journal.pcbi.1000140, 2467474, 18670624.
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.8
-
-
Zotenko, E.1
Mestre, J.2
O'Leary, D.P.3
Przytycka, T.M.4
-
46
-
-
44449108785
-
Regulation of growth factor signaling by FRS2 family docking/scaffold adaptor proteins
-
10.1111/j.1349-7006.2008.00840.x, 18452557
-
Gotoh N. Regulation of growth factor signaling by FRS2 family docking/scaffold adaptor proteins. Cancer Sci 2008, 99(7):1319-1325. 10.1111/j.1349-7006.2008.00840.x, 18452557.
-
(2008)
Cancer Sci
, vol.99
, Issue.7
, pp. 1319-1325
-
-
Gotoh, N.1
-
47
-
-
54849372300
-
Endocytosis and intracellular trafficking of ErbBs
-
2605728, 18793634
-
Sorkin A, Goh LK. Endocytosis and intracellular trafficking of ErbBs. Exp Cell Res 2008, 314(17):3093-3106. 2605728, 18793634.
-
(2008)
Exp Cell Res
, vol.314
, Issue.17
, pp. 3093-3106
-
-
Sorkin, A.1
Goh, L.K.2
-
48
-
-
55849103180
-
Quantitative proteomics and phosphoproteomics reveal novel insights into complexity and dynamics of the EGFR signaling network
-
10.1002/pmic.200800204, 18846509
-
Morandell S, Stasyk T, Skvortsov S, Ascher S, Huber LA. Quantitative proteomics and phosphoproteomics reveal novel insights into complexity and dynamics of the EGFR signaling network. Proteomics 2008, 8(21):4383-4401. 10.1002/pmic.200800204, 18846509.
-
(2008)
Proteomics
, vol.8
, Issue.21
, pp. 4383-4401
-
-
Morandell, S.1
Stasyk, T.2
Skvortsov, S.3
Ascher, S.4
Huber, L.A.5
-
49
-
-
77951120513
-
The two faces of metallothionein in carcinogenesis: photoprotection against UVR-induced cancer and promotion of tumour survival
-
10.1039/b9pp00155g, 20354655
-
McGee HM, Woods GM, Bennett B, Chung RS. The two faces of metallothionein in carcinogenesis: photoprotection against UVR-induced cancer and promotion of tumour survival. Photochem Photobiol Sci 2010, 9(4):586-596. 10.1039/b9pp00155g, 20354655.
-
(2010)
Photochem Photobiol Sci
, vol.9
, Issue.4
, pp. 586-596
-
-
McGee, H.M.1
Woods, G.M.2
Bennett, B.3
Chung, R.S.4
-
50
-
-
34347241740
-
Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates
-
10.1186/1471-2164-8-153, 1899500, 17555589
-
Liu F, Jenssen TK, Trimarchi J, Punzo C, Cepko CL, Ohno-Machado L, Hovig E, Patrick Kuo W. Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics 2007, 8:153. 10.1186/1471-2164-8-153, 1899500, 17555589.
-
(2007)
BMC Genomics
, vol.8
, pp. 153
-
-
Liu, F.1
Jenssen, T.K.2
Trimarchi, J.3
Punzo, C.4
Cepko, C.L.5
Ohno-Machado, L.6
Hovig, E.7
Patrick Kuo, W.8
-
51
-
-
38349088960
-
Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data
-
10.1186/1471-2105-8-412, 2204045, 17961233
-
Chen J, Hsueh HM, Delongchamp R, Lin CJ, Tsai CA. Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data. BMC Bioinformatics 2007, 8:412. 10.1186/1471-2105-8-412, 2204045, 17961233.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 412
-
-
Chen, J.1
Hsueh, H.M.2
Delongchamp, R.3
Lin, C.J.4
Tsai, C.A.5
-
52
-
-
52649157765
-
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
-
10.1093/nar/gkn425, 2532726, 18660515
-
Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36(16):e105. 10.1093/nar/gkn425, 2532726, 18660515.
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.16
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
53
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
10.1073/pnas.091062498, 33173, 11309499
-
Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98(9):5116-5121. 10.1073/pnas.091062498, 33173, 11309499.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.9
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
54
-
-
12344330424
-
LimmaGUI: a graphical user interface for linear modeling of microarray data
-
10.1093/bioinformatics/bth449, 15297296
-
Wettenhall JM, Smyth GK. limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 2004, 20(18):3705-3706. 10.1093/bioinformatics/bth449, 15297296.
-
(2004)
Bioinformatics
, vol.20
, Issue.18
, pp. 3705-3706
-
-
Wettenhall, J.M.1
Smyth, G.K.2
-
55
-
-
0035733108
-
The control of the false discovery rate in multiple testing under dependency
-
Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Annals of Statistics 2001, 29(4):1165-1188.
-
(2001)
Annals of Statistics
, vol.29
, Issue.4
, pp. 1165-1188
-
-
Benjamini, Y.1
Yekutieli, D.2
-
56
-
-
33644874819
-
From genomics to chemical genomics: new developments in KEGG
-
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, (34 Database):D354-357.
-
(2006)
Nucleic Acids Res
, Issue.34
-
-
Kanehisa, M.1
Goto, S.2
Hattori, M.3
Aoki-Kinoshita, K.F.4
Itoh, M.5
Kawashima, S.6
Katayama, T.7
Araki, M.8
Hirakawa, M.9
-
57
-
-
37549057612
-
GlobalANCOVA: exploration and assessment of gene group effects
-
10.1093/bioinformatics/btm531, 18024976
-
Hummel M, Meister R, Mansmann U. GlobalANCOVA: exploration and assessment of gene group effects. Bioinformatics 2008, 24(1):78-85. 10.1093/bioinformatics/btm531, 18024976.
-
(2008)
Bioinformatics
, vol.24
, Issue.1
, pp. 78-85
-
-
Hummel, M.1
Meister, R.2
Mansmann, U.3
-
58
-
-
0002294347
-
A simple sequentially rejective multiple test procedure
-
Holm S. A simple sequentially rejective multiple test procedure. Scand J Statist 1979, 6:65-70.
-
(1979)
Scand J Statist
, vol.6
, pp. 65-70
-
-
Holm, S.1
|