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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 2314 to 2363 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
1157 ERCC2 tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] Low confidence 201.354 196.761 1.02334
1158 DIAPH1 diaphanous protein homolog 1 (diaphanous-related formin 1) (drf1). [swissprot;acc:o60610] 200.185 195.622 1.02333
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] High confidence 221.877 216.167 1.02641
1159 HPD 4-hydroxyphenylpyruvate dioxygenase (ec 1.13.11.27) (4hppd) (hpd) (hppdase). [swissprot;acc:p32754] Low confidence 203.422 198.786 1.02332
PROSC proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] High confidence 170.28 165.898 1.02641
1160 OGDH 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] 208.55 214.041 1.02633
SLC25A20 mitochondrial carnitine/acylcarnitine carrier protein (carnitine/acylcarnitine translocase) (cac). [swissprot;acc:o43772] Low confidence 201.192 196.61 1.02331
1161 no value kappa b-ras 1. [refseq;acc:nm_020345] High confidence 220.758 215.097 1.02632
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Low confidence 199.768 195.217 1.02331
1162 ATP6V0A4 atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] 192.287 187.907
NKIRAS2 i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] High confidence 220.758 215.097 1.02632
1163 LSM1 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Low confidence 201.482 196.897 1.02329
SNAPAP snare associated protein snapin. [refseq;acc:nm_012437] High confidence 220.758 215.097 1.02632
1164 ARF3 adp-ribosylation factor 3. [swissprot;acc:p16587] Low confidence 202.869 198.252 1.02329
TLE4 transducin-like enhancer protein 4. [swissprot;acc:q04727] High confidence 219.438 213.818 1.02628
1165 ARF4 adp-ribosylation factor 4. [swissprot;acc:p18085] Low confidence 202.831 198.216 1.02328
TLE3 transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] High confidence 219.401 213.785 1.02627
1166 SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Low confidence 201.081 196.508 1.02327
TLE2 transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] High confidence 219.374 213.759 1.02627
1167 EN2 homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] 219.399 213.784 1.02626
RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Low confidence 200.738 196.177 1.02325
1168 CXXC1 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] High confidence 219.399 213.784 1.02626
NOL5A nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Low confidence 201.212 196.641 1.02325
1169 ABT1 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] High confidence 219.399 213.784 1.02626
REXO4 xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Low confidence 200.521 195.967 1.02324
1170 no value cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] High confidence 219.399 213.784 1.02626
ATP6V0A1 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] Low confidence 192.255 187.889 1.02324
1171 CFL1 cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528] 201.061 196.497 1.02323
HECW1 hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] High confidence 219.399 213.784 1.02626
1172 no value transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 219.375 213.767 1.02623
SLC30A3 zinc transporter 3 (znt-3). [swissprot;acc:q99726] Low confidence 204.466 199.824 1.02323
1173 DPH1 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] High confidence 229.243 235.246 1.02619
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Low confidence 201.084 196.52 1.02322
1174 COPE coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] High confidence 187.964 192.849 1.02599
DIAPH3 diaphanous protein homolog 3 (diaphanous-related formin 3) (drf3) (fragment). [swissprot;acc:q9nsv4] Low confidence 200.258 195.713 1.02322
1175 ATP6V0C vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] High confidence 218.186 212.672 1.02593
CFL2 cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281] Low confidence 201.033 196.473 1.02321
1176 DSTN destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] 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

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/