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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Gene Rank description Value Type red Network Comparison Type Interaction Map network_comparison Filtered green
Results: HTML CSV LaTeX Showing element 6458 to 6507 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
Network Comparison Type
network_comparison
green
808 60s ribosomal protein l31. [swissprot;acc:p12947] Measured 4708.61 Divided 1.11003 5226.71
atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] Rooted 62.416 1.06435 58.6426
beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] Ranked 212.386 1.04425 221.785
calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Rooted 65.1843 Subtracted 4.0893 69.2736
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Measured 779.167 611.163 1390.33
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Squared 17254.4 3963.7 21218.1
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] 24818.5 Divided 1.16273 28857.3
809 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Rooted 82.1701 Subtracted 4.0886 86.2587
diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] Ranked 233.298 9.273 242.571
grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] Squared 15511.8 Divided 1.16255 18033.2
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 17256.5 Subtracted 3963.1 21219.6
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Measured 6435.94 609.81 7045.75
syntaxin 16 (syn16). [swissprot;acc:o14662] Ranked 212.386 Divided 1.04425 221.785
ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Rooted 62.416 1.06435 58.6426
wd-repeat protein 3. [swissprot;acc:q9unx4] Measured 4039.81 1.11001 4484.22
810 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] Ranked 212.386 1.04425 221.785
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Rooted 82.1685 Subtracted 4.0884 86.2569
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Ranked 240.194 9.237 230.957
grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] Squared 15511.8 Divided 1.16255 18033.2
jm1 protein. [refseq;acc:nm_014008] Measured 5794.8 1.10923 6427.79
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Squared 17257.5 Subtracted 3962.8 21220.3
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Measured 6435.02 609.63 7044.65
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Rooted 51.7169 Divided 1.06433 55.044
811 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] 73.9102 1.06415 78.6514
adiponectin receptor 2. [refseq;acc:nm_024551] Measured 3153.1 Subtracted 609.46 3762.56
atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] 6000.07 Divided 1.10917 6655.11
casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Ranked 240.194 Subtracted 9.237 230.957
cyclin c. [swissprot;acc:p24863] Squared 30140.2 3962.6 34102.8
swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077] 15511.8 Divided 1.16255 18033.2
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Ranked 212.386 1.04425 221.785
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Rooted 51.0091 Subtracted 4.0818 55.0909
812 alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920] Ranked 212.386 Divided 1.04425 221.785
atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Rooted 51.6795 1.06413 54.9937
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] 60.4376 Subtracted 4.0522 64.4898
puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] Measured 5745.61 609.14 6354.75
putatative 28 kda protein. [refseq;acc:nm_020143] Ranked 227.241 9.226 236.467
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Squared 17861.2 3960.6 21821.8
swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078] 15511.8 Divided 1.16255 18033.2
target of myb protein 1. [swissprot;acc:o60784] Measured 5640.79 1.10904 6255.85
813 adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] Ranked 212.386 1.04425 221.785
cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Rooted 51.7273 1.06404 55.0399
huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] Measured 5641.11 1.109 6255.99
leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] 5745.61 Subtracted 609.14 6354.75
mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Rooted 60.4385 4.0515 64.49
similar to trna synthetase class ii. [refseq;acc:nm_152268] Squared 22293.8 3948.8 26242.6
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] 15511.8 Divided 1.16255 18033.2
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Ranked 228.599 Subtracted 9.2 219.399
814 delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] Squared 22223.1 3929.3 26152.4
dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] Measured 5745.61 609.14 6354.75
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Squared 6585.44 Divided 1.16243 7655.13

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/