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 2680 to 2729 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1340 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Low confidence 8165.01 8451.45 1.03508
1341 alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] High confidence 5887.82 6354.58 1.07928
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Low confidence 8165.01 8451.45 1.03508
1342 dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] High confidence 5887.86 6354.51 1.07926
rw1 protein (fragment). [swissprot;acc:q92545] Low confidence 8165.01 8451.45 1.03508
1343 dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627] High confidence 5887.86 6354.5 1.07925
potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Low confidence 8097.5 8381.53 1.03508
1344 cbf1 interacting corepressor. [refseq;acc:nm_004882] 7869.56 8145.53 1.03507
elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] High confidence 5887.86 6354.5 1.07925
1345 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] 5887.88 6354.47
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Low confidence 7869.56 8145.53 1.03507
1346 alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] High confidence 5887.89 6354.45 1.07924
ubiquitin-protein ligase nedd-4 (ec 6.3.2.-). [swissprot;acc:p46934] Low confidence 8081.72 8365.17 1.03507
1347 molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] 7618.5 7885.61 1.03506
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] High confidence 6153.36 6640.77 1.07921
1348 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936]
molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] Low confidence 7618.5 7885.61 1.03506
1349 myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] 8103.31 8387.38
potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] High confidence 6153.36 6640.77 1.07921
1350 cda14. [refseq;acc:nm_016570] Low confidence 7436.18 7696.79 1.03505
tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] High confidence 6783.78 7320.39 1.0791
1351 dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564] 6105.23 6587.88 1.07906
myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] Low confidence 8101.7 8385.49 1.03503
1352 dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734] High confidence 6104.11 6586.48 1.07902
myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] Low confidence 8101.6 8385.37 1.03503
1353 cyclin c. [swissprot;acc:p24863] High confidence 6200.93 6690.57 1.07896
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Low confidence 8101.88 8385.7 1.03503
1354 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] High confidence 6036.22 6512.64 1.07893
dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507] Low confidence 8079.85 8362.51 1.03498
1355 calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [swissprot;acc:q13554] 8095.22 8378.39
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] High confidence 5783.9 6240.19 1.07889
1356 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] 5657.71 6103.57 1.07881
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Low confidence 7846.74 8121.14 1.03497
1357 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] High confidence 5657.71 6103.54 1.0788
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] Low confidence 8276.6 8566.03 1.03497
1358 adenosine deaminase (ec 3.5.4.4) (adenosine aminohydrolase). [swissprot;acc:p00813] 8000.32 8280.09
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] High confidence 5657.71 6103.54 1.0788
1359 dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Low confidence 8078.78 8361.23 1.03496
1360 calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] High confidence 5657.72 6103.52 1.07879
dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750] Low confidence 8077.72 8359.95 1.03494
1361 calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] High confidence 5657.72 6103.52 1.07879
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Low confidence 8111.19 8394.63 1.03494
1362 phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9]
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] High confidence 6322.75 6820.5 1.07872
1363 nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307]
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Low confidence 8292.26 8582.02 1.03494
1364 protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] High confidence 5815.14 6272.66 1.07868
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Low confidence 7527.23 7790.05 1.03492
1365 gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] High confidence 5799.14 6255.04 1.07862

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/