Class information for:
Level 1: RNA SEQ//TRANSCRIPTOME ASSEMBLY//RNA SEQUENCING

Basic class information
Class id #P Avg. number of
references		 Database coverage
of references
7400 1371 38.7 86%


Bar chart of Publication_year

Last years might be incomplete

Hierarchy of classes
The table includes all classes above and classes immediately below the current class.


Cluster id Level Cluster label #P
0 4 BIOCHEMISTRY & MOLECULAR BIOLOGY//CELL BIOLOGY//ONCOLOGY 4064930
90 3       MATHEMATICAL & COMPUTATIONAL BIOLOGY//BIOINFORMATICS//BMC BIOINFORMATICS 77178
1101 2             BIOINFORMATICS//COPY NUMBER VARIATION//NEXT GENERATION SEQUENCING 9808
7400 1                   RNA SEQ//TRANSCRIPTOME ASSEMBLY//RNA SEQUENCING 1371

Terms with highest relevance score


rank Term termType Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 RNA SEQ authKW 669080 20% 11% 268
2 TRANSCRIPTOME ASSEMBLY authKW 103911 1% 33% 14
3 RNA SEQUENCING authKW 82274 4% 8% 48
4 TRANSCRIPTOME authKW 82064 9% 3% 127
5 ANIM PROD RD address 66812 0% 100% 3
6 DESEQ2 authKW 66812 0% 100% 3
7 SPLICING GRAPH authKW 66812 0% 100% 3
8 DE NOVO ASSEMBLY authKW 64017 2% 11% 26
9 RNA SEQ DATA ANALYSIS authKW 59386 0% 67% 4
10 DIFFERENTIAL EXPRESSION ANALYSIS authKW 50893 1% 29% 8

Web of Science journal categories


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 Mathematical & Computational Biology 35631 30% 0% 406
2 Biotechnology & Applied Microbiology 22194 53% 0% 733
3 Biochemical Research Methods 12984 33% 0% 447
4 Genetics & Heredity 10191 36% 0% 495
5 Biochemistry & Molecular Biology 1078 26% 0% 361
6 Statistics & Probability 399 5% 0% 64
7 Multidisciplinary Sciences 306 3% 0% 38
8 Plant Sciences 36 4% 0% 54
9 Biology 23 2% 0% 26
10 Evolutionary Biology 21 1% 0% 17

Address terms


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 ANIM PROD RD 66812 0% 100% 3
2 CLIN GENET BIOINFORMAT 50108 0% 75% 3
3 AGRILIFE GENOM SERV 44541 0% 100% 2
4 CHAIR BIOINFORMAT GRP 40085 0% 60% 3
5 GENOM GENE EXP S 34791 0% 31% 5
6 STATE FO T TREE GENET BREEDING 29693 0% 67% 2
7 SYST PHARMACOL BIOMARKERS 29693 0% 67% 2
8 HUB BIOINFORMAT BIOSTAT 28630 0% 43% 3
9 KOREA ZOONOSIS KOZRI 28630 0% 43% 3
10 OMICS SCI 26128 1% 13% 9

Journals


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 BMC GENOMICS 43647 10% 1% 137
2 BIOINFORMATICS 43303 11% 1% 144
3 BMC BIOINFORMATICS 29593 7% 1% 100
4 GENOME BIOLOGY 16433 3% 2% 47
5 GENOME RESEARCH 13575 2% 2% 29
6 NATURE METHODS 8187 2% 1% 25
7 STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY 6327 1% 2% 12
8 JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 4911 1% 2% 9
9 BRIEFINGS IN BIOINFORMATICS 3856 1% 2% 11
10 NUCLEIC ACIDS RESEARCH 3596 6% 0% 81

Author Key Words


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class		 LCSH search Wikipedia search
1 RNA SEQ 669080 20% 11% 268 Search RNA+SEQ Search RNA+SEQ
2 TRANSCRIPTOME ASSEMBLY 103911 1% 33% 14 Search TRANSCRIPTOME+ASSEMBLY Search TRANSCRIPTOME+ASSEMBLY
3 RNA SEQUENCING 82274 4% 8% 48 Search RNA+SEQUENCING Search RNA+SEQUENCING
4 TRANSCRIPTOME 82064 9% 3% 127 Search TRANSCRIPTOME Search TRANSCRIPTOME
5 DESEQ2 66812 0% 100% 3 Search DESEQ2 Search DESEQ2
6 SPLICING GRAPH 66812 0% 100% 3 Search SPLICING+GRAPH Search SPLICING+GRAPH
7 DE NOVO ASSEMBLY 64017 2% 11% 26 Search DE+NOVO+ASSEMBLY Search DE+NOVO+ASSEMBLY
8 RNA SEQ DATA ANALYSIS 59386 0% 67% 4 Search RNA+SEQ+DATA+ANALYSIS Search RNA+SEQ+DATA+ANALYSIS
9 DIFFERENTIAL EXPRESSION ANALYSIS 50893 1% 29% 8 Search DIFFERENTIAL+EXPRESSION+ANALYSIS Search DIFFERENTIAL+EXPRESSION+ANALYSIS
10 RNA SEQ DATA 47154 0% 35% 6 Search RNA+SEQ+DATA Search RNA+SEQ+DATA

Core articles
The table includes core articles in the class. The following variables is taken into account for the relevance score of an article in a cluster c:
(1) Number of references referring to publications in the class.
(2) Share of total number of active references referring to publications in the class.
(3) Age of the article. New articles get higher score than old articles.
(4) Citation rate, normalized to year.


Rank Reference # ref.
in cl.		 Shr. of ref. in
cl.		 Citations
1 TRAPNELL, C , ROBERTS, A , GOFF, L , PERTEA, G , KIM, D , KELLEY, DR , PIMENTEL, H , SALZBERG, SL , RINN, JL , PACHTER, L , (2012) DIFFERENTIAL GENE AND TRANSCRIPT EXPRESSION ANALYSIS OF RNA-SEQ EXPERIMENTS WITH TOPHAT AND CUFFLINKS.NATURE PROTOCOLS. VOL. 7. ISSUE 3. P. 562 -578 29 71% 2089
2 CONESA, A , MADRIGAL, P , TARAZONA, S , GOMEZ-CABRERO, D , CERVERA, A , MCPHERSON, A , SZCZESNIAK, MW , GAFFNEY, DJ , ELO, LL , ZHANG, XG , ET AL (2016) A SURVEY OF BEST PRACTICES FOR RNA-SEQ DATA ANALYSIS.GENOME BIOLOGY. VOL. 17. ISSUE . P. - 86 45% 23
3 LI, B , DEWEY, CN , (2011) RSEM: ACCURATE TRANSCRIPT QUANTIFICATION FROM RNA-SEQ DATA WITH OR WITHOUT A REFERENCE GENOME.BMC BIOINFORMATICS. VOL. 12. ISSUE . P. - 29 76% 1329
4 HAAS, BJ , PAPANICOLAOU, A , YASSOUR, M , GRABHERR, M , BLOOD, PD , BOWDEN, J , COUGER, MB , ECCLES, D , LI, B , LIEBER, M , ET AL (2013) DE NOVO TRANSCRIPT SEQUENCE RECONSTRUCTION FROM RNA-SEQ USING THE TRINITY PLATFORM FOR REFERENCE GENERATION AND ANALYSIS.NATURE PROTOCOLS. VOL. 8. ISSUE 8. P. 1494 -1512 29 67% 734
5 SONESON, C , DELORENZI, M , (2013) A COMPARISON OF METHODS FOR DIFFERENTIAL EXPRESSION ANALYSIS OF RNA-SEQ DATA.BMC BIOINFORMATICS. VOL. 14. ISSUE . P. - 26 96% 182
6 ZHENG, CL , KAWANE, S , BOTTOMLY, D , WILMOT, B , (2014) ANALYSIS CONSIDERATIONS FOR UTILIZING RNA-SEQ TO CHARACTERIZE THE BRAIN TRANSCRIPTOME.BRAIN TRANSCRIPTOME. VOL. 116. ISSUE . P. 21 -54 80 50% 0
7 FINOTELLO, F , DI CAMILLO, B , (2015) MEASURING DIFFERENTIAL GENE EXPRESSION WITH RNA-SEQ: CHALLENGES AND STRATEGIES FOR DATA ANALYSIS.BRIEFINGS IN FUNCTIONAL GENOMICS. VOL. 14. ISSUE 2. P. 130 -142 49 68% 10
8 ANDERS, S , MCCARTHY, DJ , CHEN, YS , OKONIEWSKI, M , SMYTH, GK , HUBER, W , ROBINSON, MD , (2013) COUNT-BASED DIFFERENTIAL EXPRESSION ANALYSIS OF RNA SEQUENCING DATA USING R AND BIOCONDUCTOR.NATURE PROTOCOLS. VOL. 8. ISSUE 9. P. 1765-1786 34 63% 203
9 LOVE, MI , HUBER, W , ANDERS, S , (2014) MODERATED ESTIMATION OF FOLD CHANGE AND DISPERSION FOR RNA-SEQ DATA WITH DESEQ2.GENOME BIOLOGY. VOL. 15. ISSUE 12. P. - 24 60% 297
10 TANG, M , SUN, JQ , SHIMIZU, K , KADOTA, K , (2015) EVALUATION OF METHODS FOR DIFFERENTIAL EXPRESSION ANALYSIS ON MULTI-GROUP RNA-SEQ COUNT DATA.BMC BIOINFORMATICS. VOL. 16. ISSUE . P. - 41 87% 1

Classes with closest relation at Level 1


Rank Class id link
1 2013 GENOME ASSEMBLY//BIOINFORMATICS//VARIANT CALLING
2 19974 SINGLE CELL RNA SEQ//SINGLE CELL RNA SEQUENCING//SINGLE CELL TRANSCRIPTOMICS
3 19243 TRANS SPLICING//SPLICED LEADER//CHIMERIC RNA
4 4702 CHIP SEQ//ENHANCER//PEAK CALLING
5 8478 EQTL//GENETICAL GENOMICS//EQTL MAPPING
6 16034 SERIAL ANALYSIS OF GENE EXPRESSION//SAGE//GLGI
7 19783 EXPRESSION EVOLUTION//TRANS REGULATION//CIS REGULATORY DIVERGENCE
8 785 SR PROTEINS//ALTERNATIVE SPLICING//POLYPYRIMIDINE TRACT BINDING PROTEIN
9 2901 BMC BIOINFORMATICS//MICROARRAY IMAGE//BIOINFORMATICS
10 35793 RIBOTAG//S100A10//4SU

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