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 red Filtered Interaction Map network_comparison green
Results: HTML CSV LaTeX Showing element 3682 to 3731 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
red
Interaction Map
network_comparison
green
1169 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] 219.399 High confidence 1.02626 213.784
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] 200.521 Low confidence 1.02324 195.967
1170 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] 219.399 High confidence 1.02626 213.784
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] 192.255 Low confidence 1.02324 187.889
1171 cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528] 201.061 1.02323 196.497
hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] 219.399 High confidence 1.02626 213.784
1172 transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 219.375 1.02623 213.767
zinc transporter 3 (znt-3). [swissprot;acc:q99726] 204.466 Low confidence 1.02323 199.824
1173 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 229.243 High confidence 1.02619 235.246
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 201.084 Low confidence 1.02322 196.52
1174 coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] 187.964 High confidence 1.02599 192.849
diaphanous protein homolog 3 (diaphanous-related formin 3) (drf3) (fragment). [swissprot;acc:q9nsv4] 200.258 Low confidence 1.02322 195.713
1175 cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281] 201.033 1.02321 196.473
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] 218.186 High confidence 1.02593 212.672
1176 destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] 201.013 Low confidence 1.02319 196.457
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] 218.186 High confidence 1.02593 212.672
1177 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]
sodium/calcium exchanger 1 precursor (na(+)/ca(2+)-exchange protein 1). [swissprot;acc:p32418] 203.938 Low confidence 1.02318 199.317
1178 delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] 218.186 High confidence 1.02593 212.672
sodium/calcium exchanger 2 precursor (na(+)/ca(2+)-exchange protein 2). [swissprot;acc:q9upr5] 203.938 Low confidence 1.02318 199.317
1179 cellular modulator of immune recognition. [refseq;acc:nm_145021] 218.186 High confidence 1.02593 212.672
methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] 201.447 Low confidence 1.02318 196.884
1180 sodium/calcium exchanger 3 precursor (na(+)/ca(2+)-exchange protein 3) (fragment). [swissprot;acc:p57103] 203.938 199.317
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] 218.186 High confidence 1.02593 212.672
1181 gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326]
rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] 201.302 Low confidence 1.02317 196.744
1182 neurocalcin delta. [swissprot;acc:p29554] 225.104 High confidence 1.02589 230.931
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] 206.598 Low confidence 1.02315 201.924
1183 neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076] 225.103 High confidence 1.02588 230.928
tyrosine-protein kinase ryk precursor (ec 2.7.1.112). [swissprot;acc:p34925] 203.427 Low confidence 1.02315 198.825
1184 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] 216.729 High confidence 1.02586 222.334
iroquois-class homeodomain protein irx-3 (iroquois homeobox protein 3) (fragment). [swissprot;acc:p78415] 195.226 Low confidence 1.02313 190.812
1185 iroquois-class homeodomain protein irx-5 (iroquois homeobox protein 5) (irx-2a). [swissprot;acc:p78411]
visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235] 225.094 High confidence 1.02585 230.913
1186 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 218.402 1.02582 212.904
iroquois-class homeodomain protein irx-2 (iroquois homeobox protein 2) (fragment). [swissprot;acc:q9bzi1] 195.226 Low confidence 1.02313 190.812
1187 iroquois-class homeodomain protein irx-1 (iroquois homeobox protein 1) (fragment). [swissprot;acc:p78414]
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] 218.402 High confidence 1.02582 212.904
1188 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] 202.963 Low confidence 1.02311 198.378
1189 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 209.649 High confidence 1.02565 204.406
iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] 195.344 Low confidence 1.02311 190.932
1190 bleomycin hydrolase (ec 3.4.22.40) (blm hydrolase) (bmh) (bh). [swissprot;acc:q13867] 202.963 198.378
ubiquitin. [swissprot;acc:p02248] 209.6 High confidence 1.02558 204.372
1191 upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] 220.742 215.237
zinc finger protein gli3. [swissprot;acc:p10071] 203.052 Low confidence 1.02311 198.466
1192 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 199.02 1.02309 194.529
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] 220.742 High confidence 1.02558 215.237
1193 lbp-9. [refseq;acc:nm_014553]
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] 201.092 Low confidence 1.02309 196.553

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/