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 525 to 574 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
Interaction Map
red
green
network_comparison
66 mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Ranked Low confidence 221.902 200.783 1.10518
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Measured High confidence 1991.03 3221.38 1.61795
septin 10 isoform 1. [refseq;acc:nm_144710] Squared Low confidence 74803.9 94281 1.26038
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Measured 4900.7 5555.81 1.13368
67 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] High confidence 6475.5 10307.5 1.59177
brachyury protein (t protein). [swissprot;acc:o15178] Rooted Low confidence 61.687 68.2003 1.10559
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked High confidence 267.14 336.075 1.25805
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Measured Low confidence 12176.9 13781.8 1.1318
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Squared High confidence 219048 129762 1.68808
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Rooted 63.8686 47.2654 1.35128
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Ranked Low confidence 165.535 149.799 1.10505
septin 6. [swissprot;acc:q14141] Squared 74378.4 93531.9 1.25751
68 60s ribosomal protein l37a. [swissprot;acc:p12751] Ranked 239.692 217.005 1.10455
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Measured High confidence 6475.5 10307.5 1.59177
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Rooted 63.8686 47.2654 1.35128
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Ranked 267.139 336.075 1.25805
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Squared 219048 129762 1.68808
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Measured Low confidence 19498.1 17265.4 1.12932
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Rooted 55.9786 61.8641 1.10514
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Squared 27909.1 35068.7 1.25653
69 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Measured 6991.78 7848.45 1.12253
amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Rooted 60.7884 67.1136 1.10405
delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [swissprot;acc:p30038] Squared 80538.1 64191.7 1.25465
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Ranked High confidence 267.14 336.075 1.25805
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Squared 219048 129762 1.68808
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Rooted 27.9136 37.2872 1.33581
spermatogenesis associated 6. [refseq;acc:nm_019073] Measured 6475.5 10307.5 1.59177
testis-specific protein tex28. [swissprot;acc:o15482] Ranked Low confidence 259.517 235.017 1.10425
70 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Measured High confidence 6475.5 10307.5 1.59177
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Rooted 27.9136 37.2872 1.33581
guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Ranked 267.142 336.074 1.25804
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Squared 219048 129762 1.68808
phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] Low confidence 80538.1 64191.7 1.25465
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Rooted 61.9982 68.2337 1.10058
y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] Measured 6991.78 7848.45 1.12253
71 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Squared 63411.7 51068.8 1.24169
cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Ranked 230.944 209.149 1.10421
cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Measured 6991.78 7848.45 1.12253
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Rooted High confidence 27.9136 37.2872 1.33581
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Ranked 267.144 336.073 1.25802
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Squared 219048 129762 1.68808
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Measured 4556.78 2945.26 1.54716
tbp-associated factor 2; taf2 rna polymerase ii, tata box binding protein (tbp)-associated factor, 150 kd; tata box binding protein (tbp)-associated factor, rna polymerase ii, b, 150kd; cofactor of initiator function, 150kd subunit. [refseq;acc:nm_003184] Rooted Low confidence 59.6397 65.6325 1.10048
72 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Ranked High confidence 267.144 336.073 1.25802
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Squared 219048 129762 1.68808
mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Rooted Low confidence 63.1259 69.4305 1.09987
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] High confidence 27.9136 37.2872 1.33581
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Squared Low confidence 63404.8 51065.9 1.24163
set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Ranked 230.944 209.149 1.10421

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/