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 Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2275 to 2324 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1138 high-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9a (ec 3.1.4.17). [swissprot;acc:o76083] Low confidence 187.917 183.608 1.02347
vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] High confidence 218.484 212.675 1.02731
1139 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034]
solute carrier family 36 member 1; proton / amino acid symporter; lysosomal amino acid transporter 1. [refseq;acc:nm_078483] Low confidence 187.917 183.608 1.02347
1140 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] 187.8 183.496 1.02346
dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] High confidence 218.484 212.675 1.02731
1141 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972]
histone h1.5 (histone h1a). [swissprot;acc:p16401] Low confidence 198.047 193.51 1.02345
1142 histone h1.4 (histone h1b). [swissprot;acc:p10412] 198.05 193.513
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] High confidence 218.484 212.675 1.02731
1143 histone h1.1. [swissprot;acc:q02539] Low confidence 198.054 193.517 1.02344
secretory pathway component sec31b-1. [refseq;acc:nm_015490] High confidence 218.484 212.675 1.02731
1144 dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989] Low confidence 203.991 199.319 1.02344
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] High confidence 218.484 212.675 1.02731
1145 u6 snrna-associated sm-like protein lsm3 (mds017). [swissprot;acc:q9y4z1] Low confidence 201.836 197.216 1.02343
vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] High confidence 218.481 212.675 1.0273
1146 dna replication licensing factor mcm7 (cdc47 homolog) (p1.1-mcm3). [swissprot;acc:p33993] Low confidence 201.363 196.754 1.02343
vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] High confidence 218.483 212.676 1.0273
1147 inositol polyphosphate-5-phosphatase; phosphatidylinositol polyphosphate 5-phosphatase type iv; phosphatidylinositol (4,5) bisphosphate 5-phosphatase. [refseq;acc:nm_019892] Low confidence 198.92 194.368 1.02342
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] High confidence 208.651 203.109 1.02729
1148 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Low confidence 200.371 195.785 1.02342
ubiquitin. [swissprot;acc:p02248] High confidence 209.061 203.518 1.02724
1149 bystin. [swissprot;acc:q13895] 239.505 233.185 1.0271
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Low confidence 203.665 199.007 1.02341
1150 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 178.634 174.552 1.02339
sorting nexin 1. [swissprot;acc:q13596] High confidence 209.868 215.522 1.02694
1151 metaxin 1. [swissprot;acc:q13505] 199.552 204.925 1.02693
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Low confidence 199.769 195.206 1.02338
1152 epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] High confidence 221.939 216.143 1.02682
transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] Low confidence 197.295 192.791 1.02336
1153 epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] High confidence 221.93 216.146 1.02676
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Low confidence 199.769 195.209 1.02336
1154 homeobox protein otx2. [swissprot;acc:p32243] 205.64 200.948 1.02335
inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] High confidence 224.307 230.242 1.02646
1155 homeobox protein otx1. [swissprot;acc:p32242] Low confidence 205.629 200.937 1.02335
inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] High confidence 224.307 230.242 1.02646
1156 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9]
cone-rod homeobox protein. [swissprot;acc:o43186] Low confidence 205.625 200.934 1.02335
1157 ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] High confidence 224.307 230.242 1.02646
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 diaphanous protein homolog 1 (diaphanous-related formin 1) (drf1). [swissprot;acc:o60610] 200.185 195.622 1.02333
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 4-hydroxyphenylpyruvate dioxygenase (ec 1.13.11.27) (4hppd) (hpd) (hppdase). [swissprot;acc:p32754] Low confidence 203.422 198.786 1.02332
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] High confidence 170.28 165.898 1.02641
1160 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] 208.55 214.041 1.02633
mitochondrial carnitine/acylcarnitine carrier protein (carnitine/acylcarnitine translocase) (cac). [swissprot;acc:o43772] Low confidence 201.192 196.61 1.02331
1161 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 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
i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] High confidence 220.758 215.097 1.02632

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/