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 11714 to 11763 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2427 mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Measured 5333.6 5531.41 1.03709
Rooted 59.9715 59.1233 1.01435
proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] Ranked 212.374 211.618 1.00357
2428 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 192.871 193.555 1.00355
ba207c16.2 (fragment). [sptrembl;acc:q9nql7] Rooted 67.052 68.0131 1.01433
fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Measured 7243.19 7509.81 1.03681
phosducin-like protein (phlp). [swissprot;acc:q13371] Squared 20163.2 21432.5 1.06295
2429 adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] Rooted 60.43 61.2917 1.01426
esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Ranked 192.871 193.555 1.00355
fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] Measured 7243.19 7509.81 1.03681
replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Squared 20163.2 21432.5 1.06295
2430 epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333] Ranked 217.873 218.644 1.00354
n-acetylglutamate synthase. [refseq;acc:nm_153006] Rooted 59.1706 60.0135 1.01425
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Measured 7243.07 7509.58 1.0368
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Squared 20163.2 21432.5 1.06295
2431 fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] Measured 7242.75 7508.98 1.03676
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Squared 20163.2 21432.5 1.06295
proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] Ranked 213.048 212.3 1.00352
thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Rooted 58.1803 59.0062 1.0142
2432 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] Ranked 215.807 216.556 1.00347
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] Rooted 58.1803 59.0062 1.0142
dna repair protein rad52 homolog. [swissprot;acc:p43351] Squared 20163.2 21432.5 1.06295
gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] Measured 8154.48 8453.84 1.03671
2433 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Ranked 217.366 218.117 1.00346
gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] Squared 50637.2 47640.6 1.0629
mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] Measured 4585.86 4753.26 1.0365
stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] Rooted 58.1803 59.0062 1.0142
2434 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Squared 20156.4 21423.3 1.06285
methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Ranked 213.021 212.286 1.00346
stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] Rooted 58.1803 59.0062 1.0142
wd repeat domain 26. [refseq;acc:nm_025160] Measured 6423.46 6655.9 1.03619
2435 activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] 3669.33 3797.78 1.03501
rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062] Squared 26153.4 27795 1.06277
zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78] Rooted 68.4616 69.4316 1.01417
zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] Ranked 217.366 218.117 1.00346
2436 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Measured 3708.67 3584.47 1.03465
elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639] Ranked 217.366 218.117 1.00346
kruppel-related zinc finger protein hckrox. [refseq;acc:nm_015872] Rooted 68.4601 69.4303 1.01417
succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] Squared 27332.6 29048.4 1.06277
2437 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Measured 3708.67 3584.47 1.03465
guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774] Ranked 219.361 220.116 1.00344
peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] Rooted 68.4624 69.4323 1.01417
rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] Squared 26331.9 27982.7 1.06269
2438 abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910] 26574.1 28224 1.06209
adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] Rooted 60.4127 61.2677 1.01415
proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789] Ranked 214.049 213.323 1.0034
rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701] Measured 7139.06 7384.85 1.03443
2439 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] Ranked 220.681 221.425 1.00337
adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747] Rooted 60.4127 61.2677 1.01415
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Measured 3754.39 3629.51 1.03441

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/