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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green 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
red
green
network_comparison
15 camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] Ranked Subtracted Low confidence 0 13109 18516 5407
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Squared High confidence 21723.1 39570.4 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 39.8493 52.9343 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 286.347 238.454 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 0.0279126 5.80317 207.905
Rooted 2.24657 8.64796 3.84941
gbp protein isoform a. [refseq;acc:nm_017870] High confidence 1 23.9771 42.4773 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 22422 14964 7458
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 1 266.863 336.19 69.327
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared 219048 129762 89286
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Low confidence 122475 159767 37292
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Measured 15464.1 17572.7 2108.6
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Squared 0 180093 189590 9497
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Measured Divided 485.286 2740.13 5.64642
Squared High confidence 1.73869 19295.9 11098
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Ranked 1 56.7244 75.3948 1.32914
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Measured Subtracted 21591.5 27904.5 6313
myotubularin related protein 8. [refseq;acc:nm_017677] Low confidence 0 3888.6 4823.8 935.2
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Ranked Divided 1 255.046 202.362 1.26035
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Rooted High confidence 0 4.24264 0.00001 424264
sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] Subtracted Low confidence 46.9228 36.3465 10.5763
sperm associated antigen 7. [refseq;acc:nm_004890] Squared Divided 1 209554 136572 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 10 156 15.6
Ranked 19403 11267 1.72211
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Rooted Subtracted Low confidence 1 31.8641 47.6922 15.8281
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Measured Divided 1983.91 3007.85 1.51612
ubiquitin protein ligase. [refseq;acc:nm_130466] Rooted Subtracted High confidence 0 24.0391 11.258 12.7811
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Measured 7981.68 6685.11 1296.57
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Divided 1 2671 871 3.06659
Squared 1688.58 179.56 9.40399
16 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Measured Low confidence 21185 28492 1.34491
bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Squared 333556 475119 1.42441
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Ranked 0 7395 11625 1.57201
cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Rooted Subtracted 12.4097 22.2036 9.7939
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Ranked Divided High confidence 12170.7 20670.6 1.69839
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Measured Subtracted 1 24260.3 18172.1 6088.2
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared 0 21165.1 38499.2 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 1 284.798 237.743 47.055
dystrophin. [swissprot;acc:p11532] Rooted High confidence 0 17.8026 5.12693 12.6757
gbp protein isoform a. [refseq;acc:nm_017870] Low confidence 1 31.8923 47.7107 15.8184
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Ranked High confidence 266.864 336.184 69.32
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared Low confidence 122475 159767 37292
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Measured 15464.1 17572.7 2108.6
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Squared 0 178510 187889 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 1 203.673 182.638 21.035
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Squared 219048 129762 89286
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Ranked Divided 56.7252 75.3954 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 29.3087 7.61577 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 8852.4 7572.88 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 0.00001 0.0766864 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/