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 2308 to 2357 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1154 PPA1 inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] Divided 224.307 230.242 1.02646
1155 ATP6V0B vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Subtracted 218.186 212.672 5.514
PPA2 inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] Divided 224.307 230.242 1.02646
1156 AIPL1 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9]
SGCG gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Subtracted 218.186 212.672 5.514
1157 AIP ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] Divided 224.307 230.242 1.02646
UBP1 upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Subtracted 220.742 215.237 5.505
1158 EPS8L2 epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] Divided 221.877 216.167 1.02641
TFCP2 transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Subtracted 220.742 215.237 5.505
1159 PROSC proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Divided 170.28 165.898 1.02641
TFCP2L1 lbp-9. [refseq;acc:nm_014553] Subtracted 220.742 215.237 5.505
1160 OGDH 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] Divided 208.55 214.041 1.02633
SFRS3 splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Subtracted 220.742 215.237 5.505
1161 no value adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 218.402 212.904 5.498
kappa b-ras 1. [refseq;acc:nm_020345] Divided 220.758 215.097 1.02632
1162 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] Subtracted 218.402 212.904 5.498
NKIRAS2 i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] Divided 220.758 215.097 1.02632
1163 ARL4A adp-ribosylation factor-like protein 4. [swissprot;acc:p40617] Subtracted 218.402 212.904 5.498
SNAPAP snare associated protein snapin. [refseq;acc:nm_012437] Divided 220.758 215.097 1.02632
1164 OGDH 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] Subtracted 208.55 214.041 5.491
TLE4 transducin-like enhancer protein 4. [swissprot;acc:q04727] Divided 219.438 213.818 1.02628
1165 CASP7 caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] Subtracted 233.942 228.46 5.482
TLE3 transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Divided 219.401 213.785 1.02627
1166 CASP3 apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574] Subtracted 233.942 228.46 5.482
TLE2 transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Divided 219.374 213.759 1.02627
1167 EN2 homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] 219.399 213.784 1.02626
KCTD10 mstp028 protein. [refseq;acc:nm_031954] Subtracted 219.042 213.6 5.442
1168 CXXC1 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Divided 219.399 213.784 1.02626
SMARCB1 swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Subtracted 219.03 213.604 5.426
1169 ABT1 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Divided 219.399 213.784 1.02626
TNFAIP1 tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Subtracted 219.023 213.606 5.417
1170 no value cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Divided 219.399 213.784 1.02626
KCTD13 polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Subtracted 219.022 213.607 5.415
1171 DYNLT3 t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] 173.475 178.889 5.414
HECW1 hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Divided 219.399 213.784 1.02626
1172 no value transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 219.375 213.767 1.02623
MRE11A double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Subtracted 173.475 178.889 5.414
1173 COPB1 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] 171.341 176.746 5.405
DPH1 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] Divided 229.243 235.246 1.02619
1174 C11orf2 chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] Subtracted 214.364 219.759 5.395
COPE coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] Divided 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
KIF13A kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Subtracted 214.364 219.759 5.395
1176 COG2 conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746]
SGCZ sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Divided 218.186 212.672 1.02593
1177 no value kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Subtracted 214.364 219.759 5.395
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] Divided 218.186 212.672 1.02593
1178 MTX1 metaxin 1. [swissprot;acc:q13505] Subtracted 199.552 204.925 5.373
SGCD delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Divided 218.186 212.672 1.02593
1179 no value keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Subtracted 219.356 224.723 5.367

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/