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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3927 to 3976 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1964 endothelial-derived gene 1. [refseq;acc:nm_025205] Subtracted 202.211 200.18 2.031
rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] Divided 211.633 213.703 1.00978
1965 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] 224.432 222.258
homolog of yeast maf1. [refseq;acc:nm_032272] Subtracted 209.539 207.529 2.01
1966 oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] Divided 211.633 213.703 1.00978
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Subtracted 209.539 207.529 2.01
1967 choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] Divided 211.632 213.702 1.00978
tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] Subtracted 209.539 207.529 2.01
1968 tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5]
voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] Divided 211.633 213.703 1.00978
1969 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175] Subtracted 209.539 207.529 2.01
1970 importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] Divided 211.62 213.683 1.00975
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Subtracted 205.876 203.873 2.003
1971 creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] Divided 198.258 196.346 1.00974
rh type c glycoprotein. [refseq;acc:nm_016321] Subtracted 196.88 198.88 2
1972 regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] Divided 219.777 217.659 1.00973
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Subtracted 214.775 216.769 1.994
1973 putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] 223.168 221.176 1.992
wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5] Divided 214.611 212.546 1.00972
1974 rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407] Subtracted 196.925 198.91 1.985
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Divided 214.611 212.546 1.00972
1975 rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] Subtracted 196.932 198.914 1.982
wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558] Divided 214.611 212.546 1.00972
1976 rest corepressor. [refseq;acc:nm_015156]
very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975] Subtracted 191.424 193.404 1.98
1977 homolog of yeast maf1. [refseq;acc:nm_032272] Divided 209.539 207.529 1.00969
solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094] Subtracted 191.401 193.38 1.979
1978 delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062] 191.411 193.39
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Divided 209.539 207.529 1.00969
1979 lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] Subtracted 191.411 193.39 1.979
tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] Divided 209.539 207.529 1.00969
1980 solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] Subtracted 191.406 193.385 1.979
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] Divided 209.539 207.529 1.00969
1981 d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
disrupter of silencing 10. [refseq;acc:nm_020368] Subtracted 191.411 193.39 1.979
1982 40s ribosomal protein s28. [swissprot;acc:p25112] Divided 200.343 198.427 1.00966
very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031] Subtracted 191.41 193.389 1.979
1983 lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] Divided 219.25 217.175 1.00955
solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254] Subtracted 191.408 193.387 1.979
1984 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Divided 219.26 217.193 1.00952
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] Subtracted 191.415 193.394 1.979
1985 lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] 225.015 223.041 1.974
mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] Divided 219.26 217.193 1.00952
1986 65 kda yes-associated protein (yap65). [swissprot;acc:p46937]
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Subtracted 196.964 198.935 1.971
1987 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]
lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] Divided 225.022 222.9 1.00952
1988 9 kda protein. [swissprot;acc:p13994] 219.26 217.193
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Subtracted 196.965 198.936 1.971

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
- 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.
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