University scores highest in 16 out of 47 subjects, with Oxford placed second and LSE leapfrogging St Andrews into third

Cambridge has topped the Guardian University Guide league table for the second year running, while Oxford has come second and the London School of Economics has climbed a place to third.

St Andrews, rated third last year, is now in fourth place, while Warwick rises a place to fifth. University College London (UCL), Durham, Lancaster, Bath and Exeter make up the top 10.

The guide is accompanied by rankings showing how universities perform across the main subject areas, published in full on Tuesday. Cambridge dominates across the board, coming top in 16 out of 47 subjects including biosciences, chemical engineering, computer science, maths, medicine and veterinary science.

Oxford came top in seven subjects including business studies, chemistry, economics, law and physics.

In the subject tables, there was a strong performance by UCL, which ranked top in six subjects including archaeology, architecture and English. But UCL dropped a place in the overall table to sixth due to a poor ranking in mechanical engineering and a few other subjects.

Universities are ranked according to spending per student; their student/staff ratio; graduate career prospects; what grades applicants need; a value-added score that compares students' entry qualifications with their final degree results; and how happy final-year students are with their courses, based on the annual National Student Survey.

The tables are compiled by an independent consultancy, Intelligent Metrix.

Brian Oldham, a financial analyst at King's College London and a member of the review group for the tables, acknowledged that the NSS is subjective. He said: "Students at a university that generally has a high reputation may be more demanding in the quality of teaching they expect.

"On the other hand, students that are at a university that it is lower down in the pecking order may receive teaching that exceeds their prior expectations and give marks higher than would be achieved under any objective measure."

The use of entry grades implies that students with the strongest qualifications will go to the university that is best for their subject. It also means that some institutions with access programmes – admitting lower-performing candidates on the basis of potential – score less highly. The use of a value-added score, measuring the impact of teaching, offers a counterweight.

Most of the shifts in this year's league table are due to changing levels of student satisfaction. Sussex dropped to 27th place from 11th after students in English and geography became significantly less happy with their departments. Stirling dropped from 44th to 67th after value-added scores in business and law declined.

Aberystwyth fell in six subjects, with declines in all performance measures. It drops from 50th place to 81st.

Among the climbers is Brunel, up from 82nd to 44th, taking the top spot for social work. Chester went from 80th to 52nd, with student satisfaction results driving improved ratings in biosciences, history, law and psychology. The career prospects of its biosciences graduates also improved. Coventry rose from 63rd to 46th, with student survey results a major factor.

Bolton, the University of Abertay, Dundee and London Met are the lowest ranked universities in the overall table. Bolton will charge a range of fees up to a maximum of £8,400.

Cambridge is not listed in the tables for physics or chemistry because it offers a natural sciences tripos, and the data could not be adequately split according to the constituent parts of this inter-disciplinary course.

All of the public English universities in the Guardian's top 20 will charge the maximum fee of £9,000 for new undergraduates from this September, except for the LSE, which will charge £8,500.

Dr Wendy Piatt, director general of the Russell Group, said: "Our universities do well in these and other tables but students should remember all league tables have their limitations and should look beyond rankings when choosing a degree course.

"Russell Group universities excel at research but even though this is not measured in these tables our universities have still performed well. Teaching is one of our top priorities and we believe the combination of world-class teaching and research excellence in our universities creates the ideal learning environment. Our universities offer a broad range of study options from Arabic to Zoology and Mechanical Engineering to Medicine.

"Our students work with their field's leading experts, have access to first-rate libraries and facilities, are part of a highly motivated and talented peer group and often engage in cutting-edge research themselves.

"Employability is particularly important to potential students in the current climate. Employers rank six Russell Group universities in the top 13 universities in the world, and Russell Group graduates receive on average a 10 per cent salary 'top-up' over those from other universities.

"Our universities have higher than average levels of student satisfaction and the lowest drop-out rates – and we are constantly working to improve the student experience."

There are 16 English universities in the top 20: Cambridge, Oxford, LSE, Warwick, UCL, Durham, Lancaster, Bath, Exeter, Loughborough, Surrey, Imperial College, Buckingham, York, Bristol and Leicester.

Buckingham is a private university, which will charge £22,500 for a two-year degree. Students eligible for a government-backed loan will be able to borrow up to £12,000 over the two years.The Guardian University Guide 2013 league table of universities is published today. Subject tables will be available from Tuesday morning.

• For more details on the methodology used for the Guardian University Guide tables, please read our methodology guide. Individual queries should be sent to data@intelligentmetrix.co.uk