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 2513 to 2562 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
315 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] Squared Subtracted 31819.7 39222.2 7402.5
glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Rooted 59.6399 51.9242 7.7157
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Ranked 88.2482 110.265 22.0168
methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Divided 244.126 268.604 1.10027
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Rooted 95.0526 85.3206 1.11406
proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Squared 71576.8 56326.7 1.27074
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Measured 21370.8 17896.5 1.19413
vav proto-oncogene. [swissprot;acc:p15498] Subtracted 6644.99 7707.8 1062.81
316 gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Rooted 59.6399 51.9242 7.7157
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Ranked 88.2482 110.265 22.0168
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Rooted Divided 95.0526 85.3206 1.11406
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Squared 28918.3 36746 1.27068
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Ranked 242.694 267.017 1.10022
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Squared Subtracted 44848.2 52108.3 7260.1
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Measured Divided 21370.8 17896.5 1.19413
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Subtracted 6603.41 7664.65 1061.24
317 adiponectin receptor 2. [refseq;acc:nm_024551] Divided 3153.1 3762.56 1.19329
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Rooted 95.0526 85.3206 1.11406
glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Subtracted 59.6399 51.9242 7.7157
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Ranked 88.2482 110.265 22.0168
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Squared Divided 33982.3 43159.1 1.27005
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Ranked 224.445 204.044 1.09998
vav-3 protein. [swissprot;acc:q9ukw4] Measured Subtracted 6647.43 7706.18 1058.75
zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] Squared 44848.2 52108.3 7260.1
318 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Measured 7485.08 8543.66 1058.58
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Rooted 38.8223 46.4975 7.6752
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Ranked 88.2482 110.265 22.0168
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Divided 242.011 266.18 1.09987
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Squared 46739.9 59134.5 1.26518
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Rooted 95.0526 85.3206 1.11406
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Measured 34190.9 40795.8 1.19318
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Squared Subtracted 44848.2 52108.3 7260.1
319 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Measured 7477 8532.02 1055.02
60s ribosomal protein l19. [swissprot;acc:p14118] Ranked Divided 240.73 264.729 1.09969
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Rooted Subtracted 53.4993 45.9227 7.5766
maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] Squared 37147.5 44372.1 7224.6
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Ranked 88.2482 110.265 22.0168
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Squared Divided 46739.9 59134.5 1.26518
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Measured 20911 24908.5 1.19117
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Rooted 49.0663 54.4978 1.1107
320 40s ribosomal protein s29. [swissprot;acc:p30054] 50.2784 45.294 1.11005
carboxypeptidase b precursor. [refseq;acc:nm_020361] Subtracted 77.5801 70.0182 7.5619
coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Squared 49280.5 42272.7 7007.8
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Ranked Divided 241.892 265.96 1.0995
epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Squared 87971.9 69563.1 1.26463
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Ranked Subtracted 88.2482 110.265 22.0168
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Measured Divided 20911 24908.5 1.19117
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Subtracted 10263.8 11318.6 1054.8
321 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Ranked Divided 241.892 265.959 1.09949
fibulin-1 precursor. [swissprot;acc:p23142] Squared Subtracted 44407.1 51387.4 6980.3

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/