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 Value Type description Network Comparison Type Interaction Map red green network_comparison Filtered
Results: HTML CSV LaTeX Showing element 451 to 500 of 77072 in total
Rank
Value Type
description
Network Comparison Type
Interaction Map
red
green
network_comparison
Filtered
15 Measured myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Subtracted High confidence 21591.5 27904.5 6313 1
myotubularin related protein 8. [refseq;acc:nm_017677] Low confidence 3888.6 4823.8 935.2 0
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] Divided High confidence 10 156 15.6
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Low confidence 1983.91 3007.85 1.51612 1
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Subtracted High confidence 7981.68 6685.11 1296.57 0
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Divided 2671 871 3.06659 1
Ranked adenomatous polyposis coli like. [refseq;acc:nm_005883] Low confidence 12074.1 7597.61 1.5892 0
camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] Subtracted 13109 18516 5407
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] 286.347 238.454 47.893 1
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] High confidence 22422 14964 7458 0
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 266.863 336.19 69.327 1
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Divided 56.7244 75.3948 1.32914
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Low confidence 255.046 202.362 1.26035
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] High confidence 19403 11267 1.72211 0
Squared cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted 21723.1 39570.4 17847.3
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] Divided Low confidence 0.0279126 5.80317 207.905
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Subtracted High confidence 219048 129762 89286 1
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Low confidence 122475 159767 37292
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] 180093 189590 9497 0
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Divided High confidence 1.73869 19295.9 11098
sperm associated antigen 7. [refseq;acc:nm_004890] Low confidence 209554 136572 1.53438 1
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 1688.58 179.56 9.40399
Rooted amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Subtracted 80.4705 101.526 21.0555
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] Divided Low confidence 39.8493 52.9343 1.32836
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] 2.24657 8.64796 3.84941 0
gbp protein isoform a. [refseq;acc:nm_017870] High confidence 23.9771 42.4773 1.77158 1
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 4.24264 0.00001 424264 0
sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] Subtracted Low confidence 46.9228 36.3465 10.5763
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 31.8641 47.6922 15.8281 1
ubiquitin protein ligase. [refseq;acc:nm_130466] High confidence 24.0391 11.258 12.7811 0
16 Measured 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided Low confidence 21185 28492 1.34491 1
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted High confidence 24260.3 18172.1 6088.2
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence 15464.1 17572.7 2108.6
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] High confidence 8852.4 7572.88 1279.52 0
protein kinase, lysine deficient 3. [refseq;acc:nm_020922] Divided Low confidence 125 704.5 5.636
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] High confidence 1 15 15
protein x 0004. [refseq;acc:nm_016301] 2671 871 3.06659 1
vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21] Subtracted Low confidence 8926.33 9808 881.67 0
Ranked beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Divided 7395 11625 1.57201
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] High confidence 12170.7 20670.6 1.69839
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] Subtracted Low confidence 284.798 237.743 47.055 1
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] High confidence 266.864 336.184 69.32
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Divided 56.7252 75.3954 1.32913
ptd016 protein. [refseq;acc:nm_016125] Subtracted 18050 11234 6816 0
sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] Low confidence 7435.56 12191.6 4756.04
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Divided 305.472 247.246 1.2355 1
Squared bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 333556 475119 1.42441
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted High confidence 21165.1 38499.2 17334.1 0
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Low confidence 122475 159767 37292 1
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] 178510 187889 9379 0

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/