Copyright
©The Author(s) 2021.
World J Hepatol. Jan 27, 2021; 13(1): 94-108
Published online Jan 27, 2021. doi: 10.4254/wjh.v13.i1.94
Published online Jan 27, 2021. doi: 10.4254/wjh.v13.i1.94
Table 1 List of the final 85 selected publications for each layer of data. For each publication the number of hepatocellular carcinoma samples and controls and the platform used for the analysis are reported
Gene expression | |||||
No. | year | PMID | HCC (n) | Controls (n) | GEO dataset |
1 | 2004 | 17393520 | 35 | 13 | GSE6764 |
2 | 2008 | 18504433 | 11 | 2 | GSE6222 |
3 | 2008 | 18923165 | 80 | 82 | GSE10143 |
4 | 2009 | 19098997 | 47 | 58 | GSE14323 |
5 | 2009 | 19861515 | 16 | 47 | GSE17967 |
6 | 2011 | 21320499 | 34 | 34 | GSE20140 (GSE10141, GSE10140) |
7 | 2011 | 21712445 | 40 | 40 | GSE28248 |
8 | 2013 | 23691139 | 15 | 15 | GSE17548 |
9 | 2013 | 23800896 | GSE36376_276; GSE25097_211 | GSE36376_247; GSE25097_283 | GSE36376, GSE25097 |
10 | 2014 | 24498002 | 46 | 46 | GSE47595 |
11 | 2014 | 24564407 | 45 | 45 | GSE45114 |
12 | 2014 | 25093504 | 39 | 40 | GSE57958 |
13 | 2014 | 25141867 | 11 | 11 | GSE55092 |
14 | 2014 | 25376302 | 18 | 18 | GSE60502 |
15 | 2014 | 25536056 | 72 | 72 | GSE39791 |
16 | 2015 | 25666192 | 132 | 132 | GSE54236 |
17 | 2015 | 25645722 | 228 | 168 | GSE63898 |
18 | 2016 | 27499918 | 60 | 60 | GSE64041 |
19 | 2016 | 25964079 | 26 | 20 | GSE54238 |
Proteomics | |||||
No. | year | PMID | HCC (n) | Controls (n) | |
1 | 2004 | 14726492 | 8 | 8 | |
2 | 2008 | 19003864 | 12 | 12 | |
3 | 2005 | 15759316 | 10 | 10 | |
4 | 2005 | 16097030 | 14 | 14 | |
5 | 2007 | 17627933 | 12 | 12 | |
6 | 2014 | 23621634 | 3 | 3 | |
7 | 2009 | 19562805 | 3 | 3 | |
8 | 2016 | 26709725 | 24 | 12 | |
9 | 2013 | 23589362 | 20 | 20 | |
10 | 2012 | 22813877 | 10 | 10 | |
11 | 2012 | 22082227 | 11 | 11 | |
12 | 2011 | 21631109 | 69 | 123 | |
13 | 2010 | 20230046 | 5 | 5 | |
14 | 2010 | 19956837 | 20 | 20 | |
15 | 2009 | 19715608 | 18 | 18 | |
16 | 2009 | 19535095 | 3 | 3 | |
17 | 2009 | 19161326 | 80 | 80 | |
18 | 2004 | 15221772 | 20 | 20 | |
19 | 2003 | 14673798 | 21 | 21 | |
20 | 2003 | 14654528 | 21 | 21 | |
21 | 2002 | 12481271 | 11 | 11 | |
22 | 2013 | 23462207 | 7 | 7 | |
23 | 2005 | 16335951 | 8 | 8 | |
24 | 2006 | 16342242 | 10 | 10 | |
25 | 2011 | 22034872 | 3 | 3 | |
26 | 2005 | 15852300 | 7 | 7 | |
27 | 2011 | 21913717 | 3 | 3 | |
28 | 2007 | 17203974 | 25 | 28 | |
29 | 2007 | 17586277 | 10 | 10 | |
Whole exome sequencing | |||||
No. | year | PMID | HCC (n) | Controls (n) | GEO dataset |
1 | 2013 | 23912677 | 3 | 3 | N/A |
2 | 2014 | 24055508 | 4 | 7 | N/A |
3 | 2017 | 28323123 | 5 | 5 | N/A |
4 | 2014 | 24798001 | 231 | 231 | GSE54504 |
5 | 2012 | 22561517 | 24 | 24 | N/A |
Epigenetic_miRNAs | |||||
No. | year | PMID | HCC (n) | Controls (n) | GEO dataset |
1 | 2015 | 26190160 | 9 | 7 | N/A |
2 | 2014 | 24789420 | 10 | 9 | GSE31383 |
3 | 2014 | 24564407 | 45 | 45 | GSE10694 |
4 | 2011 | 21298008 | 73 | 73 | GSE21362 |
5 | 2008 | 18649363 | 78 | 10 | N/A |
6 | 2012 | 22135159 | 20 | 20 | N/A |
7 | 2011 | 21319996 | 94 | 94 | N/A |
8 | 2009 | 19473441 | 20 | 20 | N/A |
9 | 2009 | 19173277 | 35 | N/A | |
10 | 2007 | 18171346 | 10 | 10 | N/A |
11 | 2006 | 16331254 | 25 | 25 | N/A |
12 | 2015 | 26062888 | 30 | 30 | N/A |
13 | 2015 | 26046780 | 327 | 43 | N/A |
14 | 2015 | 25861255 | 66 | 66 | GSE54751 |
15 | 2015 | 25500075 | 6 | 6 | GSE54537 |
16 | 2014 | 24875649 | 24 | 24 | |
17 | 2013 | 23812667 | 166 | 166 | GSE31384 |
18 | 2013 | 23390000 | 9 | 17 | GSE40744 |
19 | 2012 | 23082062 | 18 | 18 | N/A |
20 | 2014 | 24586785 | 29 | 29 | N/A |
21 | 2013 | 24417970 | 78 | 78 | N/A |
Epigenetic methylation | |||||
No. | year | PMID | HCC (n) | Controls (n) | GEO dataset |
1 | 2011 | 21500188 | 13 | 12 | N/A |
2 | 2014 | 24306662 | 45 | 45 | N/A |
3 | 2014 | 25376292 | 22 | 22 | N/A |
4 | 2015 | 25945129 | 8 | 8 | GSE59260 |
5 | 2011 | 21747116 | 12 | 12 | GSE29720 |
6 | 2010 | 20165882 | 20 | 20 | GSE18081 |
7 | 2012 | 22234943 | 62 | 62 | GSE37988 |
8 | 2013 | 24012984 | 20 | 8 | GSE44970 |
9 | 2013 | 23208076 | 66 | 66 | GSE54503 |
10 | 2014 | 25093504 | 59 | 59 | GSE57956 |
11 | 2014 | 25294808 | 27 | 27 | GSE60753 |
- Citation: Bhat M, Pasini E, Pastrello C, Rahmati S, Angeli M, Kotlyar M, Ghanekar A, Jurisica I. Integrative analysis of layers of data in hepatocellular carcinoma reveals pathway dependencies. World J Hepatol 2021; 13(1): 94-108
- URL: https://www.wjgnet.com/1948-5182/full/v13/i1/94.htm
- DOI: https://dx.doi.org/10.4254/wjh.v13.i1.94