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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1162 to 1211 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    1162 NKIRAS2 i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] 220.758 215.097 1.02632
    1163 SNAPAP snare associated protein snapin. [refseq;acc:nm_012437]
    1164 TLE4 transducin-like enhancer protein 4. [swissprot;acc:q04727] 219.438 213.818 1.02628
    1165 TLE3 transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] 219.401 213.785 1.02627
    1166 TLE2 transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] 219.374 213.759
    1167 EN2 homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] 219.399 213.784 1.02626
    1168 CXXC1 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4]
    1169 ABT1 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375]
    1170 no value cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569]
    1171 HECW1 hect type e3 ubiquitin ligase. [refseq;acc:nm_015052]
    1172 no value transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 219.375 213.767 1.02623
    1173 DPH1 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 229.243 235.246 1.02619
    1174 COPE coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] 187.964 192.849 1.02599
    1175 ATP6V0C vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] 218.186 212.672 1.02593
    1176 SGCZ sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167]
    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]
    1178 SGCD delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629]
    1179 MARCH8 cellular modulator of immune recognition. [refseq;acc:nm_145021]
    1180 ATP6V0B vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437]
    1181 SGCG gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326]
    1182 NCALD neurocalcin delta. [swissprot;acc:p29554] 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
    1184 GIT1 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] 216.729 222.334 1.02586
    1185 HPCAL1 visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235] 225.094 230.913 1.02585
    1186 no value adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 218.402 212.904 1.02582
    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]
    1188 ARL4A adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
    1189 no value alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 209.649 204.406 1.02565
    1190 UBB ubiquitin. [swissprot;acc:p02248] 209.6 204.372 1.02558
    1191 UBP1 upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] 220.742 215.237
    1192 TFCP2 transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]
    1193 TFCP2L1 lbp-9. [refseq;acc:nm_014553]
    1194 SFRS3 splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152]
    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
    1196 KIF2B kinesin protein. [refseq;acc:nm_032559] 224.858 219.264 1.02551
    1197 KCTD10 mstp028 protein. [refseq;acc:nm_031954] 219.042 213.6 1.02548
    1198 FHL3 skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] 269.59 276.454 1.02546
    1199 MPHOSPH10 u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] 241.496 235.508 1.02543
    1200 SMARCB1 swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] 219.03 213.604 1.0254
    1201 SDHA succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] 210.986 216.344
    1202 DPH2 diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384] 227.274 233.041 1.02537
    1203 TNFAIP1 tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] 219.023 213.606 1.02536
    1204 KCTD13 polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] 219.022 213.607 1.02535
    1205 KIF21A ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] 224.805 219.251 1.02533
    1206 no value integral membrane protein cii-3b. [sptrembl;acc:o75609] 207.646 212.891 1.02526
    1207 SDHC succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] 207.644 212.888 1.02525
    1208 no value signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 224.878 219.342 1.02524
    1209 SDHB succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] 207.931 213.175 1.02522
    1210 KIF2A kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] 224.764 219.241 1.02519
    1211 C11orf2 chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] 214.364 219.759 1.02517

    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/