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 3758 to 3807 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1879 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Divided 212.186 214.467 1.01075
1880 calmegin precursor. [swissprot;acc:o14967] Subtracted 217.48 215.256 2.224
cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] Divided 220.852 223.225 1.01074
1881 calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] Subtracted 217.48 215.256 2.224
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Divided 210.592 208.355 1.01074
1882 60s ribosomal protein l28. [swissprot;acc:p46779] 215.896 213.61 1.0107
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Subtracted 217.48 215.256 2.224
1883 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Divided 240.317 242.881 1.01067
rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799] Subtracted 217.48 215.256 2.224
1884 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 221.607 219.386 2.221
putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] Divided 215.081 217.373 1.01066
1885 arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] 204.44 206.615 1.01064
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Subtracted 180.609 178.393 2.216
1886 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 215.853 213.639 2.214
arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] Divided 204.512 206.682 1.01061
1887 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Subtracted 180.537 178.325 2.212
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Divided 220.896 218.577 1.01061
1888 gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] Subtracted 224.264 222.055 2.209
immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] Divided 218.414 216.131 1.01056
1889 centaurin gamma 2. [swissprot;acc:q9upq3] Subtracted 220.659 218.452 2.207
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Divided 211.27 209.067 1.01054
1890 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] Subtracted 220.659 218.452 2.207
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Divided 211.314 209.111 1.01054
1891 centaurin gamma 1. [swissprot;acc:q99490] Subtracted 220.659 218.452 2.207
dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] Divided 233.828 231.395 1.01051
1892 centaurin gamma 3. [swissprot;acc:q96p47] Subtracted 220.659 218.452 2.207
kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] Divided 233.828 231.395 1.01051
1893 gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] 222.842 225.17 1.01045
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Subtracted 211.27 209.067 2.203
1894 gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Divided 222.842 225.17 1.01045
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Subtracted 211.314 209.111 2.203
1895 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] Divided 215.853 213.639 1.01036
megf11 protein. [refseq;acc:nm_032445] Subtracted 224.34 222.147 2.193
1896 lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290] Divided 199.883 197.835 1.01035
megf10 protein. [refseq;acc:nm_032446] Subtracted 224.341 222.148 2.193
1897 beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] 224.343 222.151 2.192
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Divided 199.883 197.835 1.01035
1898 lim/homeobox protein lhx4. [swissprot;acc:q969g2] 199.881 197.833
p28 ing5. [refseq;acc:nm_032329] Subtracted 215.848 218.039 2.191
1899 fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] 203.071 200.89 2.181
lim/homeobox protein lhx3. [swissprot;acc:q9ubr4] Divided 199.884 197.837 1.01035
1900 phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] Subtracted 215.745 213.564 2.181
solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094] Divided 191.401 193.38 1.01034
1901 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
phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2] Subtracted 215.745 213.564 2.181
1902 lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] Divided 191.411 193.39 1.01034
multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] Subtracted 203.071 200.89 2.181
1903 enigma protein; lim domain protein. [refseq;acc:nm_005451] 219.753 217.574 2.179
solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] Divided 191.406 193.385 1.01034
1904 eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] Subtracted 219.753 217.574 2.179

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/