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 3908 to 3957 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1954 voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] Divided 211.632 213.703 1.00979
1955 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Subtracted 180.409 182.459 2.05
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Divided 211.633 213.703 1.00978
1956 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Subtracted 180.409 182.459 2.05
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] Divided 211.633 213.703 1.00978
1957 receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] Subtracted 225.019 222.969 2.05
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557] Divided 211.633 213.703 1.00978
1958 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154]
lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290] Subtracted 199.883 197.835 2.048
1959 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] Divided 211.633 213.703 1.00978
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Subtracted 199.883 197.835 2.048
1960 epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] 225.019 222.971
golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] Divided 211.633 213.703 1.00978
1961 alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870]
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] Subtracted 225.019 222.971 2.048
1962 lim/homeobox protein lhx4. [swissprot;acc:q969g2] 199.881 197.833
methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] Divided 211.632 213.702 1.00978
1963 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] 211.633 213.703
lim/homeobox protein lhx3. [swissprot;acc:q9ubr4] Subtracted 199.884 197.837 2.047
1964 endothelial-derived gene 1. [refseq;acc:nm_025205] 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

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.
- http://analysis.yellowcouch.org/