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 6808 to 6857 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1702 protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] Rooted 62.9822 65.0473 1.03279
1703 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Ranked 216.079 219.024 1.01363
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] Rooted 62.9823 65.0473 1.03279
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Squared 2612.13 2364.75 1.10461
phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645] Measured 6326.24 6762.27 1.06892
1704 ataxin 2-binding protein. [swissprot;acc:q9nwb1] Ranked 218.514 215.577 1.01362
camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] Rooted 62.9823 65.0473 1.03279
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Squared 2612.21 2364.84 1.1046
homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] Measured 5778.4 6176.13 1.06883
1705 camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] Rooted 62.9823 65.0473 1.03279
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Squared 2612.98 2365.77 1.10449
serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172] Ranked 223.846 220.847 1.01358
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] Measured 5369.43 5738.73 1.06878
1706 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Squared 2613.08 2365.88 1.10449
immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] Ranked 223.846 220.847 1.01358
translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] Measured 5369.43 5738.73 1.06878
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Rooted 65.6831 67.835 1.03276
1707 camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 62.9889 65.0525
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Squared 2613.13 2365.94 1.10448
mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566] Ranked 221.283 218.334 1.01351
proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] Measured 5777.1 6174.15 1.06873
1708 60s acidic ribosomal protein p2. [swissprot;acc:p05387] Rooted 56.1247 54.3497 1.03266
metaxin 2. [swissprot;acc:o75431] Measured 7033.72 7516.77 1.06868
putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] Squared 24853.2 27447.8 1.1044
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Ranked 221.283 218.334 1.01351
1709 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Squared 2613.69 2366.62 1.1044
homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Ranked 198.014 195.385 1.01346
homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] Measured 5775.55 6171.79 1.06861
p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] Rooted 61.6482 63.6574 1.03259
1710 camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] Measured 5916.13 6321.77 1.06857
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] Ranked 227.225 224.21 1.01345
geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Rooted 53.8424 55.5929 1.03251
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Squared 2614.02 2367 1.10436
1711 biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] Ranked 218.436 215.553 1.01337
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Squared 2614.02 2367 1.10436
protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] Measured 5917.22 6322.72 1.06853
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Rooted 64.6674 66.7696 1.03251
1712 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] Measured 5917.23 6322.73 1.06853
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] Rooted 64.803 66.9076 1.03248
transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] Ranked 208.598 211.375 1.01331
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] Squared 13649.9 15070.2 1.10405
1713 camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] Measured 5917.23 6322.73 1.06853
katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Squared 16662.1 18391.9 1.10382
proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] Rooted 64.3126 66.4016 1.03248
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Ranked 206.823 204.111 1.01329
1714 armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 206.549 203.844 1.01327
camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] Measured 5917.23 6322.73 1.06853
dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1] Squared 24923.8 27509.9 1.10376
peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] Rooted 64.7728 66.8682 1.03235
1715 camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] Measured 5918.48 6323.83 1.06849

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/