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 network_comparison green
    Results: HTML CSV LaTeX Showing element 1175 to 1224 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		network_comparison
    		green
    1175 ATP6V0C vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] 218.186 1.02593 212.672
    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 1.02589 230.931
    1183 HPCA neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076] 225.103 1.02588 230.928
    1184 GIT1 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] 216.729 1.02586 222.334
    1185 HPCAL1 visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235] 225.094 1.02585 230.913
    1186 no value adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 218.402 1.02582 212.904
    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 1.02565 204.406
    1190 UBB ubiquitin. [swissprot;acc:p02248] 209.6 1.02558 204.372
    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 1.02554 276.493
    1196 KIF2B kinesin protein. [refseq;acc:nm_032559] 224.858 1.02551 219.264
    1197 KCTD10 mstp028 protein. [refseq;acc:nm_031954] 219.042 1.02548 213.6
    1198 FHL3 skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] 269.59 1.02546 276.454
    1199 MPHOSPH10 u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] 241.496 1.02543 235.508
    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 1.0254 213.604
    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 1.02537 233.041
    1203 TNFAIP1 tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] 219.023 1.02536 213.606
    1204 KCTD13 polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] 219.022 1.02535 213.607
    1205 KIF21A ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] 224.805 1.02533 219.251
    1206 no value integral membrane protein cii-3b. [sptrembl;acc:o75609] 207.646 1.02526 212.891
    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 1.02525 212.888
    1208 no value signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 224.878 1.02524 219.342
    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 1.02522 213.175
    1210 KIF2A kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] 224.764 1.02519 219.241
    1211 C11orf2 chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] 214.364 1.02517 219.759
    1212 KIF13A kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9]
    1213 COG2 conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746]
    1214 no value kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]
    1215 DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 218.268 1.02514 212.916
    1216 ZMIZ1 retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] 218.269 1.02513 212.918
    1217 QRSL1 glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] 211.959 1.025 217.258
    1218 FAAH fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519]
    1219 COTL1 coactosin-like protein. [swissprot;acc:q14019]
    1220 UNG uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051]
    1221 PET112L probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]
    1222 TPD52L1 tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] 206.774 1.02496 211.936
    1223 TPD52 tumor protein d52 (n8 protein). [swissprot;acc:p55327] 206.771 1.02493 211.926
    1224 FPGS folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 225.906 1.02487 231.524

    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/