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 5758 to 5807 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
938 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] Rooted 62.3618 66.0328 1.05887
glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Squared 25043.4 28913.4 1.15453
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Ranked 220.246 212.618 1.03588
939 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 216.501 224.27
dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Rooted 62.3617 66.0327 1.05887
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Squared 25044.9 28915.2 1.15453
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Measured 5859.25 6432.03 1.09776
940 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 5568.96 6113.35 1.09775
calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Ranked 212.442 205.088 1.03586
ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Rooted 62.3618 66.0328 1.05887
glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304] Squared 25108.4 28986.7 1.15446
941 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 26005.2 30020.3 1.1544
caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] Measured 4970.21 5455.34 1.09761
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Ranked 212.437 205.083 1.03586
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] Rooted 62.3618 66.0328 1.05887
942 cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] Squared 23659.9 27312.6 1.15438
grancalcin. [swissprot;acc:p28676] Ranked 212.442 205.088 1.03586
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Measured 6597.56 7240.64 1.09747
secretory pathway component sec31b-1. [refseq;acc:nm_015490] Rooted 62.3618 66.0328 1.05887
943 cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] Squared 23659.2 27311.3 1.15436
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Measured 6597.98 7241 1.09746
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Ranked 212.442 205.087 1.03586
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Rooted 62.3617 66.0327 1.05887
944 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Measured 6597.98 7241 1.09746
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Ranked 212.437 205.083 1.03586
tcd37 homolog; prune. [refseq;acc:nm_021222] Squared 23659.1 27311.1 1.15436
vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] Rooted 62.3614 66.0323 1.05886
945 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Measured 6597.98 7241 1.09746
brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Ranked 212.44 205.085 1.03586
cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] Squared 23658.7 27310.2 1.15434
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Rooted 62.409 66.0815 1.05885
946 cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] Squared 23658.5 27309.8 1.15433
histone h4. [swissprot;acc:p02304] Ranked 227.765 219.902 1.03576
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Measured 6598.37 7241.32 1.09744
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Rooted 62.4087 66.0813 1.05885
947 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Ranked 212.51 205.191 1.03567
atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] Rooted 62.4093 66.0819 1.05885
signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Measured 11797.1 10750.2 1.09738
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Squared 24999.1 28856.8 1.15431
948 caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] Measured 4633.48 5084.24 1.09728
target of myb protein 1. [swissprot;acc:o60784] Ranked 217.254 209.824 1.03541
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Rooted 62.4102 66.0829 1.05885
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] Squared 25295.5 29197.3 1.15425
949 apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574] Measured 4633.48 5084.24 1.09728
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Rooted 82.2821 87.1197 1.05879
huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] Ranked 217.253 209.826 1.0354
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Squared 27084.5 31257.9 1.15409
950 bystin. [swissprot;acc:q13895] Measured 4280.99 4697.02 1.09718
dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] Ranked 252.873 261.821 1.03539
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Rooted 82.2706 87.1037 1.05875

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/