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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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 77072 in total
Rank
description
Value Type
Network Comparison Type
Interaction Map
Filtered
green
red
network_comparison
15 camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] Ranked Subtracted Low confidence 0 18516 13109 5407
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Squared High confidence 39570.4 21723.1 17847.3
cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] Rooted Divided Low confidence 1 52.9343 39.8493 1.32836
cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] Ranked Subtracted 238.454 286.347 47.893
fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344] Squared Divided 0 5.80317 0.0279126 207.905
Rooted 8.64796 2.24657 3.84941
gbp protein isoform a. [refseq;acc:nm_017870] High confidence 1 42.4773 23.9771 1.77158
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] Ranked Subtracted 0 14964 22422 7458
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 1 336.19 266.863 69.327
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared 129762 219048 89286
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Low confidence 159767 122475 37292
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Measured 17572.7 15464.1 2108.6
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Squared 0 189590 180093 9497
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Measured Divided 2740.13 485.286 5.64642
Squared High confidence 19295.9 1.73869 11098
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Ranked 1 75.3948 56.7244 1.32914
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Measured Subtracted 27904.5 21591.5 6313
myotubularin related protein 8. [refseq;acc:nm_017677] Low confidence 0 4823.8 3888.6 935.2
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Ranked Divided 1 202.362 255.046 1.26035
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Rooted High confidence 0 0.00001 4.24264 424264
sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] Subtracted Low confidence 36.3465 46.9228 10.5763
sperm associated antigen 7. [refseq;acc:nm_004890] Squared Divided 1 136572 209554 1.53438
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Measured High confidence 0 156 10 15.6
Ranked 11267 19403 1.72211
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Rooted Subtracted Low confidence 1 47.6922 31.8641 15.8281
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Measured Divided 3007.85 1983.91 1.51612
ubiquitin protein ligase. [refseq;acc:nm_130466] Rooted Subtracted High confidence 0 11.258 24.0391 12.7811
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Measured 6685.11 7981.68 1296.57
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Divided 1 871 2671 3.06659
Squared 179.56 1688.58 9.40399
16 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Measured Low confidence 28492 21185 1.34491
bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Squared 475119 333556 1.42441
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Ranked 0 11625 7395 1.57201
cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Rooted Subtracted 22.2036 12.4097 9.7939
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Ranked Divided High confidence 20670.6 12170.7 1.69839
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Measured Subtracted 1 18172.1 24260.3 6088.2
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared 0 38499.2 21165.1 17334.1
cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] Ranked Low confidence 1 237.743 284.798 47.055
dystrophin. [swissprot;acc:p11532] Rooted High confidence 0 5.12693 17.8026 12.6757
gbp protein isoform a. [refseq;acc:nm_017870] Low confidence 1 47.7107 31.8923 15.8184
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Ranked High confidence 336.184 266.864 69.32
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared Low confidence 159767 122475 37292
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Measured 17572.7 15464.1 2108.6
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Squared 0 187889 178510 9379
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Rooted High confidence 1 182.638 203.673 21.035
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Squared 129762 219048 89286
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Ranked Divided 75.3954 56.7252 1.32913
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Rooted Low confidence 0 7.61577 29.3087 3.84842
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Measured Subtracted High confidence 7572.88 8852.4 1279.52
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Squared Divided 0.0766864 0.00001 7668.64

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/