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 24176 to 24225 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
2520 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] Rooted Subtracted 71.5034 72.1258 0.6224
2521 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] Measured Divided 5964.17 6113.96 1.02511
40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Subtracted 3708.67 3584.47 124.2
anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] Squared Divided 53510.3 50671 1.05603
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Rooted 62.4421 63.0515 1.00976
maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Subtracted 58.1063 58.7277 0.6214
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Ranked Divided 201.96 201.488 1.00234
protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Squared Subtracted 12039.4 13153.3 1113.9
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Ranked 209.143 208.659 0.484
2522 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] Squared Divided 33471.2 31713.3 1.05543
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Measured Subtracted 7181.3 7057.99 123.31
cerebral cell adhesion molecule. [refseq;acc:nm_016174] Ranked 194.349 193.871 0.478
keratin associated protein 4.4. [refseq;acc:nm_032524] Rooted Divided 62.4421 63.0514 1.00976
keratin associated protein 9.2. [refseq;acc:nm_031961] Subtracted 62.4423 63.0566 0.6143
m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Squared 24288.8 23193.7 1095.1
retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] Measured Divided 5964.17 6113.96 1.02511
unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432] Ranked 215.835 216.341 1.00234
2523 60s ribosomal protein l32. [swissprot;acc:p02433] Squared Subtracted 12314 13403.2 1089.2
apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] Ranked 216.264 215.787 0.477
dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] Measured Divided 3803.04 3710.01 1.02508
importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Ranked 201.96 201.488 1.00234
lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] Rooted Subtracted 66.145 66.7577 0.6127
skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] Measured 3634.59 3756.67 122.08
star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4] Rooted Divided 62.4421 63.0513 1.00976
transcription factor jun-d. [swissprot;acc:p17535] Squared 28267.9 26786.5 1.0553
2524 adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677] 33464.1 31711.8 1.05526
c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] Subtracted 37111.5 38198.5 1087
myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] Measured Divided 8695.15 8912.98 1.02505
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] Ranked Subtracted 212.464 211.99 0.474
ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] Rooted Divided 62.4421 63.0513 1.00976
skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192] Measured Subtracted 3633.14 3754.96 121.82
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Ranked Divided 201.96 201.488 1.00234
tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] Rooted Subtracted 66.145 66.7577 0.6127
2525 26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556] Ranked Divided 215.835 216.341 1.00234
arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] Measured 8695.15 8912.98 1.02505
chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973] Ranked Subtracted 187.853 188.326 0.473
defender against cell death 1 (dad-1). [swissprot;acc:p46966] Rooted 66.145 66.7577 0.6127
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Squared Divided 22805.9 24065.6 1.05524
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Rooted 62.4421 63.0515 1.00976
phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Squared Subtracted 28935 30015.7 1080.7
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Measured 7169.01 7047.98 121.03
2526 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] Squared 28935 30015.7 1080.7
chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197] Measured 7538.48 7417.58 120.9
high-mobility group 20a. [refseq;acc:nm_018200] Squared Divided 22834 24093.6 1.05516
lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] Rooted 58.8808 59.4552 1.00976
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Ranked Subtracted 201.96 201.488 0.472
t-complex 11. [refseq;acc:nm_018679] Rooted 66.145 66.7577 0.6127
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Ranked Divided 201.96 201.488 1.00234
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Measured 8695.15 8912.98 1.02505
2527 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] Squared Subtracted 28935 30015.7 1080.7

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/