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 4091 to 4140 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1023 protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Measured 6435.02 7044.65 1.09474
transforming protein rhoc (h9). [swissprot;acc:p08134] Ranked 205.632 199.266 1.03195
1024 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Measured 5706.5 6245.55 1.09446
m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] Rooted 48.9418 51.5408 1.0531
orphan nuclear receptor tr2. [swissprot;acc:p13056] Squared 29904.9 34332.5 1.14806
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Ranked 205.632 199.266 1.03195
1025 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] Rooted 55.3631 58.2965 1.05298
inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] Squared 22126.7 25398.5 1.14787
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Measured 5511.96 6031.95 1.09434
1026 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] Rooted 55.3631 58.2965 1.05298
inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] Squared 22126.7 25398.5 1.14787
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Measured 5509.89 6029.29 1.09427
transforming protein rhoa (h12). [swissprot;acc:p06749] Ranked 205.632 199.266 1.03195
1027 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] Squared 22126.7 25398.5 1.14787
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Rooted 52.1219 49.5013 1.05294
s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] Measured 6123.15 6700.05 1.09422
succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] Ranked 211.908 218.627 1.03171
1028 ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] Squared 22126.7 25398.5 1.14787
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Measured 5704 6241.36 1.09421
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Rooted 52.1219 49.5013 1.05294
succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7] Ranked 211.908 218.627 1.03171
1029 beta-catenin (pro2286). [swissprot;acc:p35222] Measured 5635.26 6166.09 1.0942
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] Ranked 222.364 215.535 1.03168
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Squared 31999.3 36726.8 1.14774
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Rooted 52.1219 49.5013 1.05294
1030 casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] Measured 5048.33 5523.85 1.09419
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Squared 31994.3 36720 1.1477
oligophrenin 1. [swissprot;acc:o60890] Rooted 52.1219 49.5013 1.05294
propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Ranked 222.364 215.535 1.03168
1031 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Squared 31994 36719.6 1.1477
kappa b-ras 1. [refseq;acc:nm_020345] Rooted 61.2289 64.4564 1.05271
membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] Measured 6136.99 6714.98 1.09418
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Ranked 242.978 235.518 1.03167
1032 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 186.664 180.943 1.03162
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Squared 31994 36719.6 1.1477
i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] Rooted 61.2289 64.4564 1.05271
ran binding protein 11. [refseq;acc:nm_016338] Measured 6138.91 6717.05 1.09418
1033 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Squared 31994 36719.6 1.1477
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Measured 6080.91 6653.52 1.09417
snare associated protein snapin. [refseq;acc:nm_012437] Rooted 61.2289 64.4564 1.05271
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Ranked 221.183 214.406 1.03161
1034 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Squared 31994 36719.6 1.1477
s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] Measured 6152.88 6732.12 1.09414
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Ranked 186.551 180.837 1.0316
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Rooted 58.8683 61.9622 1.05256
1035 atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] Ranked 221.682 228.68 1.03157
c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Rooted 60.6801 63.8644 1.05248
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] Measured 5054.73 5530.23 1.09407
limkain b1. [refseq;acc:nm_019081] Squared 31994 36719.6 1.1477

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/