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 201 to 250 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
13 dok-like protein. [refseq;acc:nm_024872] Rooted Divided 0 5.91608 0.00001 591608
dystrophin. [swissprot;acc:p11532] Ranked Subtracted 10232.5 18054.8 7822.3
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 1 266.856 336.233 69.377
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Divided 0 5210.5 9264.5 1.77804
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Squared Subtracted 1.73869 19295.9 19294.2
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 1 219048 129762 89286
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Measured 21591.5 27904.5 6313
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Ranked Divided 288.754 212.554 1.3585
14 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Measured Subtracted 0 10817.1 12125.1 1308
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Squared Divided 1.73869 19295.9 11098
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Measured 130.512 6.50325 20.0687
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Ranked 1 56.6768 75.3531 1.32952
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Rooted Subtracted 0 39.9124 52.9528 13.0404
dystrophin. [swissprot;acc:p11532] Ranked Divided 10232.5 18054.8 1.76446
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Subtracted 1 266.863 336.191 69.328
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared 219048 129762 89286
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Measured 21591.5 27904.5 6313
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] Rooted Divided 0 0.00001 4.24264 424264
protein cgi-147. [swissprot;acc:q9y3e5] Squared Subtracted 75129.2 94178 19048.8
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Measured Divided 1 398.5 1281.5 3.21581
Squared 37.5863 388.696 10.3414
Rooted 19.9625 35.798 1.79326
spermatogenesis associated 6. [refseq;acc:nm_019073] Subtracted 80.4705 101.526 21.0555
ubiquitin protein ligase. [refseq;acc:nm_130466] Ranked 0 7523 15339.2 7816.2
15 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Rooted 1 80.4705 101.526 21.0555
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Squared 0 21723.1 39570.4 17847.3
gbp protein isoform a. [refseq;acc:nm_017870] Rooted Divided 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
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Divided 0 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
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Rooted Divided 0 4.24264 0.00001 424264
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 10 156 15.6
Ranked 19403 11267 1.72211
ubiquitin protein ligase. [refseq;acc:nm_130466] Rooted Subtracted 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 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Ranked 0 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
dystrophin. [swissprot;acc:p11532] Rooted 17.8026 5.12693 12.6757
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Ranked 1 266.864 336.184 69.32
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 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
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Measured Subtracted 0 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/