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 29192 to 29241 of 77072 in total
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
Interaction Map
red
green
network_comparison
1152 ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] Squared Subtracted High confidence 40276.1 37105 3171.1
1153 aspartate aminotransferase, cytoplasmic (ec 2.6.1.1) (transaminase a) (glutamate oxaloacetate transaminase-1). [swissprot;acc:p17174] Rooted Low confidence 71.8379 74.5965 2.7586
connective tissue growth factor precursor (hypertrophic chondrocyte- specific protein 24). [swissprot;acc:p29279] Ranked 208.383 203.805 4.578
cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] Squared Divided High confidence 26906.6 30660.6 1.13952
delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Ranked Subtracted 218.186 212.672 5.514
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Squared Low confidence 36300.9 34239.3 2061.6
dj467n11.1 protein. [refseq;acc:nm_022091] Measured Divided 8198.49 8500.02 1.03678
epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] Ranked High confidence 221.93 216.146 1.02676
epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] Squared Low confidence 42736.9 40855.6 1.04605
meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] Measured Subtracted High confidence 5913.73 6423.98 510.25
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Rooted 56.1832 53.2244 2.9588
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Squared 26952.5 30122.8 3170.3
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Ranked Divided Low confidence 199.769 195.209 1.02336
protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] Rooted 70.7057 73.405 1.03818
scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] High confidence 59.9298 62.8125 1.0481
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Measured 5840.01 6355.56 1.08828
u5 snrnp-associated 102 kda protein (u5-102 kda protein). [swissprot;acc:o94906] Subtracted Low confidence 7721.24 8013.26 292.02
1154 5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] Rooted 75.2563 78.0139 2.7576
alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443] Squared Divided High confidence 26906.6 30660.6 1.13952
brain protein 44-like protein (hspc040) (cgi-129) (pnas-115). [swissprot;acc:q9y5u8] Ranked Subtracted Low confidence 196.378 191.803 4.575
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Rooted High confidence 56.1854 53.2272 2.9582
cellular modulator of immune recognition. [refseq;acc:nm_145021] Ranked 218.186 212.672 5.514
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Measured Low confidence 7722.06 8014.04 291.98
homeobox protein otx2. [swissprot;acc:p32243] Ranked Divided 205.64 200.948 1.02335
inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] High confidence 224.307 230.242 1.02646
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Squared Subtracted 26952.5 30122.8 3170.3
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Low confidence 47398.5 45337.1 2061.4
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Rooted Divided High confidence 59.9298 62.8125 1.0481
receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626] Squared Low confidence 42737.3 40856 1.04605
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Measured 7803.88 8090.88 1.03678
transcription factor tel-2 (ets-related protein tel2) (tel related ets factor). [swissprot;acc:q9y603] Rooted 70.7057 73.405 1.03818
tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Measured High confidence 5840.65 6355.84 1.08821
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Subtracted 6004.54 6514.24 509.7
1155 ammecr1 protein. [refseq;acc:nm_015365] Rooted Divided 59.9298 62.8125 1.0481
bone morphogenetic protein 4 precursor (bmp-4) (bmp-2b). [swissprot;acc:p12644] Squared Low confidence 40751.9 38958.4 1.04604
cbf1 interacting corepressor. [refseq;acc:nm_004882] Rooted 71.1497 73.8643 1.03815
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Squared Subtracted 36316.9 34255.6 2061.3
d-beta-hydroxybutyrate dehydrogenase, mitochondrial precursor (ec 1.1.1.30) (bdh) (3-hydroxybutyrate dehydrogenase). [swissprot;acc:q02338] Rooted 69.7681 72.5256 2.7575
dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Squared Divided High confidence 21672.8 24695.2 1.13946
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Measured Subtracted Low confidence 7722.06 8014.04 291.98
homeobox protein otx1. [swissprot;acc:p32242] Ranked Divided 205.629 200.937 1.02335
inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] High confidence 224.307 230.242 1.02646
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Squared Subtracted 26952.5 30122.8 3170.3
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] Rooted 66.4107 69.3664 2.9557
serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Measured Divided Low confidence 8031.82 8326.95 1.03675
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Ranked Subtracted 201.081 196.508 4.573
transducin-like enhancer protein 4. [swissprot;acc:q04727] Measured Divided High confidence 6270.67 6823.73 1.0882
ubiquitin-like protein smt3a. [swissprot;acc:p55854] Subtracted 5826.34 6335.98 509.64
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Ranked 218.186 212.672 5.514
1156 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Squared Divided 26905.4 30657.2 1.13944

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/