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 3180 to 3229 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
398 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Squared Subtracted 26157.6 20236.2 5921.4
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Ranked Divided 218.818 238.358 1.0893
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Subtracted 207.908 226.218 18.31
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Rooted Divided 116.707 106.044 1.10055
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Measured 5084.26 5904.1 1.16125
399 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Ranked 207.889 226.226 1.08821
cyclin g2. [swissprot;acc:q16589] Rooted 116.707 106.044 1.10055
dna repair protein rad52 homolog. [swissprot;acc:p43351] Ranked Subtracted 207.908 226.218 18.31
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Squared Divided 18929.1 23222.8 1.22683
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Measured 5201.41 4479.76 1.16109
thymic stromal co-transporter. [refseq;acc:nm_033051] Squared Subtracted 26157.6 20236.2 5921.4
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Rooted 63.2134 69.352 6.1386
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Measured 4633.92 5572.85 938.93
400 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Divided 5201.41 4479.76 1.16109
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Ranked Subtracted 207.931 226.209 18.278
cyclin g1 (cyclin g). [swissprot;acc:p51959] Rooted Divided 116.707 106.044 1.10055
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Squared 39478.8 48419 1.22646
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Measured Subtracted 1834.73 895.893 938.837
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Rooted 79.931 86.0693 6.1383
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Squared 33024.9 38867.8 5842.9
phosducin-like protein (phlp). [swissprot;acc:q13371] Ranked Divided 207.908 226.218 1.08807
401 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Measured 5201.41 4479.76 1.16109
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Squared 33044.3 40524.8 1.22638
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Measured Subtracted 1835.3 896.972 938.328
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Ranked 254.434 236.224 18.21
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Squared 28188.7 33982.7 5794
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] Ranked Divided 207.908 226.218 1.08807
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Rooted 116.707 106.044 1.10055
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Subtracted 55.9231 62.0565 6.1334
402 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Measured 6230.94 7168.2 937.26
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Squared Divided 39472 48393.1 1.22601
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Rooted 50.1918 55.2294 1.10037
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Squared Subtracted 28190.4 33984.1 5793.7
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Ranked 231.802 249.983 18.181
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Measured Divided 5201.41 4479.76 1.16109
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Rooted Subtracted 59.5128 65.604 6.0912
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Ranked Divided 207.908 226.218 1.08807
403 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Squared Subtracted 28190.4 33984.1 5793.7
calcyphosine. [swissprot;acc:q13938] Rooted 59.5128 65.604 6.0912
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Measured Divided 5201.41 4479.76 1.16109
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared 39463.9 48362.1 1.22548
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Ranked Subtracted 228.468 246.338 17.87
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Rooted Divided 59.6834 65.6741 1.10037
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Ranked 207.908 226.218 1.08807
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Measured Subtracted 6259.3 7190.91 931.61
404 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared Divided 26819.1 32855.4 1.22507
alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Subtracted 28190.4 33984.1 5793.7
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Ranked 228.463 246.33 17.867
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Rooted 59.5128 65.604 6.0912
dna repair protein rad52 homolog. [swissprot;acc:p43351] Ranked Divided 207.908 226.218 1.08807

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/