ABSTRACT: We used Affymetrix microarray profiling to analyze gene expression patterns in healthy donor liver as well as tumor and paired non-tumor tissue of HCC patients. For gene expression profiling, tumors and paired non-tumor tissues were profiled separately using a single channel array platform. Tumor and paired non-tumor samples of 22 patients of cohort1 and the normal liver pool were carried out on Affymetrix GeneChip HG-U133A 2.0 arrays (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol. The fluorescent intensities were determined with an Affymetrix GeneChip Scanner 3000, controlled by GCOS Affymetrix software. All samples of cohort2 and 42 tumor and paired non-tumor samples of cohort2 were processed on the 96 HT HG-U133A microarray platform. The fluorescent intensities were determined with an Affymetrix GeneChip HT Array Plate Scanner, controlled by GCOS Affymetrix software. Cohort 1 Training Group: LCS-005A, LCS-019A, LCS-029A, LCS-039A, LCS-039B, LCS-254A, LCS-254B, LCS-068A, LCS-068B, LCS-076A, LCS-076B, LCS-004A, LCS-004B, LCS-007A, LCS-007B, LCS-024B, LCS-042B, LCS-062B, LCS-023A, LCS-023B, LCS-067A, LCS-065A, LCS-073A, LCS-067B, LCS-065B, LCS-073B, LCS-024A, LCS-042A, LCS-062A, LCS-015A, LCS-069A, LCS-015B, LCS-069B, LCS-033A, LCS-061A, LCS-020A, LCS-045A, LCS-033B, LCS-020B, LCS-045B, LCS-057A, LCS-009A, LCS-057B, LCS-009B, LCS-049A, LCS-049B, LCS-061B, LCS-047A, LCS-047B, LCS-075A, LCS-075B, LCS-034A, LCS-034B, LCS-041A, LCS-041B, LCS-044A, LCS-044B, LCS-071A, LCS-071B, LCS-036A, LCS-064A, LCS-064B, LCS-038A, LCS-038B, LCS-002A, LCS-028B, LCS-016B, LCS-054A, LCS-063A, LCS-022A, LCS-054B, LCS-063B, LCS-022B, LCS-036B, LCS-025A, LCS-066A, LCS-027A, LCS-048A, LCS-012A, LCS-025B, LCS-066B, LCS-027B, LCS-048B, LCS-012B, LCS-051A, LCS-056A, LCS-051B, LCS-056B, LCS-028A, LCS-016A, LCS-196A, LCS-196B, LCS-072A, LCS-072B, LCS-333A, LCS-333B, LCS-339A, LCS-339B, LCS-341A, LCS-341B, LCS-343A, LCS-343B, LCS-344A, LCS-344B, LCS-346A, LCS-346B, LCS-347A, LCS-347B, LCS-393A, LCS-393B, LCS-400A, LCS-400B, LCS-401A, LCS-401B, LCS-403A, LCS-403B, LCS-406A, LCS-406B, LCS-415A, LCS-415B, LCS-424A, LCS-424B, LCS-426A, LCS-426B Cohort 2 Testing Group: LCS-079A, LCS-092A, LCS-101A, LCS-079B, LCS-092B, LCS-101B, LCS-083A, LCS-095A, LCS-102A, LCS-083B, LCS-095B, LCS-102B, LCS-085A, LCS-096A, LCS-103A, LCS-085B, LCS-096B, LCS-103B, LCS-091A, LCS-099A, LCS-105A, LCS-091B, LCS-099B, LCS-105B, LCS-122A, LCS-130A, LCS-123A, LCS-135A, LCS-123B, LCS-135B, LCS-125A, LCS-127A, LCS-136A, LCS-125B, LCS-127B, LCS-136B, LCS-122B, LCS-130B, LCS-212B, LCS-180B, LCS-183B, LCS-153B, LCS-018B, LCS-188A, LCS-185A, LCS-154A, LCS-120A, LCS-286A, LCS-086A, LCS-177A, LCS-140A, LCS-035A, LCS-188B, LCS-185B, LCS-154B, LCS-120B, LCS-286B, LCS-238B, LCS-086B, LCS-177B, LCS-035B, LCS-275B, LCS-132A, LCS-205A, LCS-274A, LCS-159A, LCS-150A, LCS-014A, LCS-227A, LCS-283A, LCS-162A, LCS-104A, LCS-272A, LCS-132B, LCS-205B, LCS-274B, LCS-159B, LCS-227B, LCS-046B, LCS-283B, LCS-272B, LCS-237A, LCS-152A, LCS-209A, LCS-211A, LCS-230A, LCS-262A, LCS-144A, LCS-158B, LCS-237B, LCS-152B, LCS-209B, LCS-211B, LCS-230B, LCS-262B, LCS-144B, LCS-212A, LCS-180A, LCS-183A, LCS-153A, LCS-018A, LCS-275A, LCS-118A, LCS-234A, LCS-210A, LCS-265A, LCS-149A, LCS-040A, LCS-169A, LCS-256A, LCS-190B, LCS-118B, LCS-234B, LCS-210B, LCS-265B, LCS-149B, LCS-040B, LCS-169B, LCS-213A, LCS-164A, LCS-223A, LCS-245A, LCS-281B, LCS-191A, LCS-171A, LCS-249A, LCS-213B, LCS-164B, LCS-245B, LCS-094B, LCS-094A, LCS-191B, LCS-171B, LCS-249B, LCS-131A, LCS-241A, LCS-074A, LCS-160A, LCS-179A, LCS-134A, LCS-224A, LCS-078A, LCS-131B, LCS-201B, LCS-074B, LCS-160B, LCS-179B, LCS-134B, LCS-147B, LCS-224B, LCS-078B, LCS-093A, LCS-253A, LCS-279A, LCS-008A, LCS-291A, LCS-281A, LCS-156A, LCS-282A, LCS-090A, LCS-151A, LCS-253B, LCS-279B, LCS-008B, LCS-172B, LCS-291B, LCS-156B, LCS-282B, LCS-090B, LCS-151B, LCS-259A, LCS-010A, LCS-264A, LCS-264B, LCS-163A, LCS-163B, LCS-089A, LCS-089B, LCS-143A, LCS-143B, LCS-199A, LCS-199B, LCS-278A, LCS-278B, LCS-119A, LCS-119B, LCS-184A, LCS-184B, LCS-203A, LCS-203B, LCS-178A, LCS-178B, LCS-284A, LCS-284B, LCS-108A, LCS-261B, LCS-043A, LCS-043B, LCS-174A, LCS-174B, LCS-166A, LCS-193A, LCS-193B, LCS-215A, LCS-215B, LCS-021A, LCS-021B, LCS-129A, LCS-129B, LCS-198A, LCS-198B, LCS-084A, LCS-084B, LCS-250A, LCS-011A, LCS-108B, LCS-011B, LCS-219A, LCS-219B, LCS-194A, LCS-194B, LCS-170A, LCS-170B, LCS-204A, LCS-204B, LCS-261A, LCS-195A, LCS-195B, LCS-200B, LCS-206A, LCS-206B, LCS-161B, LCS-145A, LCS-145B, LCS-236A, LCS-236B, LCS-270A, LCS-270B, LCS-182A, LCS-182B, LCS-197B, LCS-173B, LCS-240B, LCS-266B, LCS-167B, LCS-032B, LCS-050B, LCS-285B, LCS-031B, LCS-189A, LCS-277A, LCS-117A, LCS-267A, LCS-100A, LCS-228A, LCS-268A, LCS-222A, LCS-192A, LCS-175A, LCS-277B, LCS-117B, LCS-267B, LCS-100B, LCS-228B, LCS-268B, LCS-222B, LCS-192B, LCS-248A, LCS-121A, LCS-157A, LCS-148A, LCS-126A, LCS-260A, LCS-223B, LCS-121B, LCS-157B, LCS-148B, LCS-260B, LCS-247A, LCS-088A, LCS-243A, LCS-165A, LCS-208A, LCS-110A, LCS-146A, LCS-247B, LCS-243B, LCS-165B, LCS-208B, LCS-110B, LCS-146B, LCS-147A, LCS-173A, LCS-240A, LCS-266A, LCS-167A, LCS-032A, LCS-050A, LCS-285A, LCS-031A, LCS-106A, LCS-106B, LCS-107A, LCS-107B, LCS-109A, LCS-109B, LCS-116A, LCS-137A, LCS-137B, LCS-138A, LCS-138B, LCS-139A, LCS-139B, LCS-142A, LCS-142B, LCS-207A, LCS-231A, LCS-231B, LCS-251A, LCS-263A, LCS-263B, LCS-269A, LCS-269B, LCS-273A, LCS-273B, LCS-289A, LCS-289B, LCS-290A, LCS-290B, LCS-093B, LCS-097A, LCS-097B, LCS-104B, LCS-140B, LCS-150B, LCS-158A, LCS-161A, LCS-162B, LCS-014B, LCS-166B, LCS-172A, LCS-197A, LCS-200A, LCS-201A, LCS-216A, LCS-216B, LCS-238A, LCS-241B, LCS-046A, LCS-248B, LCS-259B, Normal1, Normal2, LCS-003B, LCS-006B, LCS-026B, LCS-128B, LCS-168B, LCS-181B, LCS-190A, X02-342A, X02-342B, X02-362A, X02-362B
