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 description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1962 to 2011 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    1962 methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] ALDH6A1 211.632 213.702 1.00978
    1963 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] HSPE1 211.633 213.703
    1964 rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] RABAC1
    1965 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] ADD1 224.432 222.258
    1966 oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] REXO2 211.633 213.703
    1967 choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] CHAT 211.632 213.702
    1968 voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] KCNAB2 211.633 213.703
    1969 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] AKR7A2
    1970 importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] KPNA6 211.62 213.683 1.00975
    1971 creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] CKM 198.258 196.346 1.00974
    1972 regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] SEC16B 219.777 217.659 1.00973
    1973 wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5] no value 214.611 212.546 1.00972
    1974 wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] WASF3
    1975 wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558] WASF1
    1976 rest corepressor. [refseq;acc:nm_015156] RCOR1
    1977 homolog of yeast maf1. [refseq;acc:nm_032272] MAF1 209.539 207.529 1.00969
    1978 tumor differentially expressed protein 2. [refseq;acc:nm_178865] SERINC2
    1979 tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] SERINC3
    1980 tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] SERINC1
    1981 d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175] PHGDH
    1982 40s ribosomal protein s28. [swissprot;acc:p25112] no value 200.343 198.427 1.00966
    1983 lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] PDLIM5 219.25 217.175 1.00955
    1984 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] EP400 219.26 217.193 1.00952
    1985 mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] MRPL24
    1986 65 kda yes-associated protein (yap65). [swissprot;acc:p46937] YAP1
    1987 lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] LIN7A 225.022 222.9
    1988 9 kda protein. [swissprot;acc:p13994] CCDC130 219.26 217.193
    1989 collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] COL4A3 219.261 217.195 1.00951
    1990 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] no value 219.26 217.194
    1991 transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] WWTR1
    1992 zasp protein (fragment). [sptrembl;acc:q9y4z3] LDB3 219.267 217.207 1.00948
    1993 huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] HIP1R 189.052 190.835 1.00943
    1994 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] COL4A3BP 189.011 190.787 1.0094
    1995 huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] HIP1 188.961 190.73 1.00936
    1996 sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] SLC5A5 204.682 202.784
    1997 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] PRODH2 204.651 202.759 1.00933
    1998 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] C15orf15 200.219 198.37 1.00932
    1999 solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] SLC5A8 204.636 202.748 1.00931
    2000 sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] SLC5A6 204.626 202.739
    2001 lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] LIN7B 225.02 222.948 1.00929
    2002 u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] SNRPB2 214.775 216.769 1.00928
    2003 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] DNALI1 208.315 206.41 1.00923
    2004 receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] ERBB4 225.019 222.969 1.00919
    2005 epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] EGFR 222.971
    2006 receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626] ERBB2
    2007 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] HACL1 222.969
    2008 receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] ERBB3
    2009 proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] CTRL 216.201 214.245 1.00913
    2010 tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] TBCC 193.517 191.766
    2011 putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305] ACOT9

    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/