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 5236 to 5285 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1309 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Squared 15397.3 17378.3 1.12866
1310 hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] 17064.6 19258.7 1.12858
mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] Measured 6051.23 6544.17 1.08146
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Ranked 226.439 221.26 1.02341
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Rooted 66.2263 69.0756 1.04302
1311 chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] Squared 24923.6 28122.8 1.12836
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Rooted 53.9101 51.6896 1.04296
exocyst complex component sec8. [swissprot;acc:q96a65] Measured 6221.22 6727.77 1.08142
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Ranked 226.439 221.26 1.02341
1312 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] Squared 24923.6 28122.8 1.12836
rad50 homolog isoform 1. [refseq;acc:nm_005732] Ranked 199.739 204.407 1.02337
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Rooted 87.3823 83.7932 1.04283
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Measured 5675.96 6136.47 1.08113
1313 60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809] 5457.14 5899.85 1.08112
aarf domain containing kinase 4. [refseq;acc:nm_024876] Squared 24923.6 28122.8 1.12836
hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] Rooted 62.0983 64.7441 1.04261
signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] Ranked 222.573 227.75 1.02326
1314 aarf domain containing kinase 1. [refseq;acc:nm_020421] Squared 24923.6 28122.8 1.12836
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Rooted 62.6357 65.2949 1.04246
signal transducer and activator of transcription 4. [swissprot;acc:q14765] Ranked 222.573 227.751 1.02326
vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Measured 5401.39 5838.63 1.08095
1315 dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] 5685.77 6145.43 1.08084
orphan nuclear receptor tr2. [swissprot;acc:p13056] Rooted 62.6353 65.2935 1.04244
signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224] Ranked 222.574 227.752 1.02326
similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Squared 27156.9 30637.1 1.12815
1316 ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Rooted 67.3577 70.2116 1.04237
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Measured 6105.93 6599.41 1.08082
signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] Ranked 222.569 227.739 1.02323
tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] Squared 26403.8 29786.4 1.12811
1317 aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] 25544.9 28816.9 1.12809
centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Ranked 206.773 202.105 1.0231
ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Rooted 67.3352 70.1873 1.04236
orphan nuclear receptor tr2. [swissprot;acc:p13056] Measured 6105.69 6599.06 1.0808
1318 histone h2b.c (h2b/c). [swissprot;acc:q99880] Squared 15254.5 17204.9 1.12786
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Rooted 67.3368 70.189 1.04236
serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] Measured 5961.97 6443.07 1.08069
signal transducer and activator of transcription 5a. [swissprot;acc:p42229] Ranked 222.546 227.673 1.02304
1319 aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Rooted 67.3443 70.1972 1.04236
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Ranked 159.75 156.153 1.02304
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Squared 15254.5 17204.9 1.12786
serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956] Measured 5961.97 6443.07 1.08069
1320 cda11 protein. [refseq;acc:nm_032026] Rooted 63.4104 66.0956 1.04235
glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] Measured 5961.97 6443.07 1.08069
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Squared 15254.5 17204.9 1.12786
signal transducer and activator of transcription 5b. [swissprot;acc:p51692] Ranked 222.544 227.667 1.02302
1321 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Rooted 62.1531 64.7775 1.04222
histone h2b. [refseq;acc:nm_175055] Squared 15254.5 17204.9 1.12786
probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] Ranked 226.347 221.259 1.023
suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Measured 6439.79 6959.21 1.08066
1322 bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]

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/