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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2351 to 2400 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
1176 DSTN destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] Low confidence 201.013 196.457 1.02319
SGCZ sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] High confidence 218.186 212.672 1.02593
1177 ACBD3 golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735]
SLC8A1 sodium/calcium exchanger 1 precursor (na(+)/ca(2+)-exchange protein 1). [swissprot;acc:p32418] Low confidence 203.938 199.317 1.02318
1178 SGCD delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] High confidence 218.186 212.672 1.02593
SLC8A2 sodium/calcium exchanger 2 precursor (na(+)/ca(2+)-exchange protein 2). [swissprot;acc:q9upr5] Low confidence 203.938 199.317 1.02318
1179 MARCH8 cellular modulator of immune recognition. [refseq;acc:nm_145021] High confidence 218.186 212.672 1.02593
MTFMT methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Low confidence 201.447 196.884 1.02318
1180 ATP6V0B vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] High confidence 218.186 212.672 1.02593
SLC8A3 sodium/calcium exchanger 3 precursor (na(+)/ca(2+)-exchange protein 3) (fragment). [swissprot;acc:p57103] Low confidence 203.938 199.317 1.02318
1181 RHAG rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] 201.302 196.744 1.02317
SGCG gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] High confidence 218.186 212.672 1.02593
1182 KCMF1 potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122] Low confidence 206.598 201.924 1.02315
NCALD neurocalcin delta. [swissprot;acc:p29554] High confidence 225.104 230.931 1.02589
1183 HPCA neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076] 225.103 230.928 1.02588
RYK tyrosine-protein kinase ryk precursor (ec 2.7.1.112). [swissprot;acc:p34925] Low confidence 203.427 198.825 1.02315
1184 GIT1 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] High confidence 216.729 222.334 1.02586
IRX3 iroquois-class homeodomain protein irx-3 (iroquois homeobox protein 3) (fragment). [swissprot;acc:p78415] Low confidence 195.226 190.812 1.02313
1185 HPCAL1 visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235] High confidence 225.094 230.913 1.02585
IRX5 iroquois-class homeodomain protein irx-5 (iroquois homeobox protein 5) (irx-2a). [swissprot;acc:p78411] Low confidence 195.226 190.812 1.02313
1186 no value adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] High confidence 218.402 212.904 1.02582
IRX2 iroquois-class homeodomain protein irx-2 (iroquois homeobox protein 2) (fragment). [swissprot;acc:q9bzi1] Low confidence 195.226 190.812 1.02313
1187 ATP6V0D1 vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] High confidence 218.402 212.904 1.02582
IRX1 iroquois-class homeodomain protein irx-1 (iroquois homeobox protein 1) (fragment). [swissprot;acc:p78414] Low confidence 195.226 190.812 1.02313
1188 ARL4A adp-ribosylation factor-like protein 4. [swissprot;acc:p40617] High confidence 218.402 212.904 1.02582
TBL3 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Low confidence 202.963 198.378 1.02311
1189 no value alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] High confidence 209.649 204.406 1.02565
IRX4 iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Low confidence 195.344 190.932 1.02311
1190 BLMH bleomycin hydrolase (ec 3.4.22.40) (blm hydrolase) (bmh) (bh). [swissprot;acc:q13867] 202.963 198.378
UBB ubiquitin. [swissprot;acc:p02248] High confidence 209.6 204.372 1.02558
1191 GLI3 zinc finger protein gli3. [swissprot;acc:p10071] Low confidence 203.052 198.466 1.02311
UBP1 upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] High confidence 220.742 215.237 1.02558
1192 ADSSL1 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Low confidence 199.02 194.529 1.02309
TFCP2 transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] High confidence 220.742 215.237 1.02558
1193 TAF7L tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Low confidence 201.092 196.553 1.02309
TFCP2L1 lbp-9. [refseq;acc:nm_014553] High confidence 220.742 215.237 1.02558
1194 MCM2 dna replication licensing factor mcm2 (nuclear protein bm28). [swissprot;acc:p49736] Low confidence 202.182 197.621 1.02308
SFRS3 splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] High confidence 220.742 215.237 1.02558
1195 FHL2 skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192] 269.608 276.493 1.02554
PLA2G6 85 kda calcium-independent phospholipase a2 (ec 3.1.1.4) (ipla2) (cai- pla2) (group vi phospholipase a2) (gvi pla2). [swissprot;acc:o60733] Low confidence 202.297 197.738 1.02306
1196 KIF2B kinesin protein. [refseq;acc:nm_032559] High confidence 224.858 219.264 1.02551
SCYE1 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Low confidence 202.297 197.738 1.02306
1197 KCTD10 mstp028 protein. [refseq;acc:nm_031954] High confidence 219.042 213.6 1.02548
PPP2R5D serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, delta isoform (pp2a, b subunit, b' delta isoform) (pp2a, b subunit, b56 delta isoform) (pp2a, b subunit, pr61 delta isoform) (pp2a, b subunit, r5 delta isoform). [swissprot;acc:q14738] Low confidence 202.297 197.738 1.02306
1198 FHL3 skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] High confidence 269.59 276.454 1.02546
PPP2R5C serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, gamma isoform (pp2a, b subunit, b' gamma isoform) (pp2a, b subunit, b56 gamma isoform) (pp2a, b subunit, pr61 gamma isoform) (pp2a, b subunit, r5 gamma isoform). [swissprot;acc:q13362] Low confidence 202.297 197.738 1.02306
1199 MPHOSPH10 u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] High confidence 241.496 235.508 1.02543
WDR4 wd-repeat protein 4. [swissprot;acc:p57081] Low confidence 204.517 199.909 1.02305
1200 ADSS adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] 198.973 194.493 1.02303
SMARCB1 swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] High confidence 219.03 213.604 1.0254

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
- Hugo is the HGNC identifier if it exists
- 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/