Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1950 to 1999 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    1950 VPS18 vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] 215.847 213.747 1.00982
    1951 TRIT1 trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] 205.876 203.873
    1952 KPNA1 importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] 211.647 213.724 1.00981
    1953 PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 125.912 127.146 1.0098
    1954 KCNAB3 voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] 211.632 213.703 1.00979
    1955 YIF1A yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] 211.633 1.00978
    1956 KCNAB1 voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722]
    1957 YIF1B similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557]
    1958 AKR7A3 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154]
    1959 ABHD3 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340]
    1960 YIPF5 golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799]
    1961 ABHD1 alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870]
    1962 ALDH6A1 methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] 211.632 213.702
    1963 HSPE1 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] 211.633 213.703
    1964 RABAC1 rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423]
    1965 ADD1 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] 224.432 222.258
    1966 REXO2 oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] 211.633 213.703
    1967 CHAT choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] 211.632 213.702
    1968 KCNAB2 voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] 211.633 213.703
    1969 AKR7A2 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
    1970 KPNA6 importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] 211.62 213.683 1.00975
    1971 CKM creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] 198.258 196.346 1.00974
    1972 SEC16B regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] 219.777 217.659 1.00973
    1973 no value wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5] 214.611 212.546 1.00972
    1974 WASF3 wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]
    1975 WASF1 wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558]
    1976 RCOR1 rest corepressor. [refseq;acc:nm_015156]
    1977 MAF1 homolog of yeast maf1. [refseq;acc:nm_032272] 209.539 207.529 1.00969
    1978 SERINC2 tumor differentially expressed protein 2. [refseq;acc:nm_178865]
    1979 SERINC3 tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530]
    1980 SERINC1 tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5]
    1981 PHGDH d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
    1982 no value 40s ribosomal protein s28. [swissprot;acc:p25112] 200.343 198.427 1.00966
    1983 PDLIM5 lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] 219.25 217.175 1.00955
    1984 EP400 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 219.26 217.193 1.00952
    1985 MRPL24 mitochondrial ribosomal protein l24. [refseq;acc:nm_024540]
    1986 YAP1 65 kda yes-associated protein (yap65). [swissprot;acc:p46937]
    1987 LIN7A lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] 225.022 222.9
    1988 CCDC130 9 kda protein. [swissprot;acc:p13994] 219.26 217.193
    1989 COL4A3 collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] 219.261 217.195 1.00951
    1990 no value collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 219.26 217.194
    1991 WWTR1 transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472]
    1992 LDB3 zasp protein (fragment). [sptrembl;acc:q9y4z3] 219.267 217.207 1.00948
    1993 HIP1R huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] 189.052 190.835 1.00943
    1994 COL4A3BP goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] 189.011 190.787 1.0094
    1995 HIP1 huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] 188.961 190.73 1.00936
    1996 SLC5A5 sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] 204.682 202.784
    1997 PRODH2 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] 204.651 202.759 1.00933
    1998 C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 200.219 198.37 1.00932
    1999 SLC5A8 solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] 204.636 202.748 1.00931

    Legend:
    - Rank is the rank after comparing the two networks
    - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
    - Hugo is the HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/