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 4458 to 4507 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2229 surfeit locus protein 5. [swissprot;acc:q15528] Divided 3650.8 3484.94 1.04759
2230 ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] Subtracted 5783.73 6048.91 265.18
zinc finger protein 291. [swissprot;acc:q9by12] Divided 3650.8 3484.94 1.04759
2231 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]
rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156] Subtracted 5783.73 6048.91 265.18
2232 polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190]
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Divided 3650.8 3484.94 1.04759
2233 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 3614.08 3450.07 1.04754
adaptor-associated kinase 1. [refseq;acc:nm_014911] Subtracted 5783.73 6048.91 265.18
2234 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] 5783.7 6048.88
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Divided 3614.07 3450.07 1.04754
2235 40s ribosomal protein s3. [swissprot;acc:p23396] 3674.29 3508.13 1.04736
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Subtracted 5783.73 6048.91 265.18
2236 rho-gtpase activating protein 10. [refseq;acc:nm_020824]
sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] Divided 5902.27 6181.21 1.04726
2237 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] 5902.26
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] Subtracted 5783.76 6048.94 265.18
2238 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Divided 5902.27 6181.21 1.04726
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Subtracted 5783.7 6048.88 265.18
2239 2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953] 5783.76 6048.94
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Divided 5902.27 6181.21 1.04726
2240 ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] Subtracted 5783.76 6048.94 265.18
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Divided 5902.27 6181.21 1.04726
2241 phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] Subtracted 5783.75 6048.93 265.18
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Divided 3670.45 3504.91 1.04723
2242 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Subtracted 5783.71 6048.89 265.18
2243 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Divided 5776.96 6049.61 1.0472
membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Subtracted 5783.76 6048.94 265.18
2244 gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915] Divided 5776.96 6049.61 1.0472
polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] Subtracted 5783.76 6048.94 265.18
2245 growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] 5783.73 6048.91
inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] Divided 5776.96 6049.61 1.0472
2246 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 6209.77 6501.99 1.04706
eyes absent homolog 3. [swissprot;acc:q99504] Subtracted 5779.66 6044.78 265.12
2247 eyes absent homolog 4. [swissprot;acc:o95677] 5784.9 6049.99 265.09
rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062] Divided 5819.36 6092.93 1.04701
2248 eyes absent homolog 2. [swissprot;acc:o00167] Subtracted 5786.15 6050.71 264.56
signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624] Divided 5833.01 6106.48 1.04688
2249 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 6834.03 7153.66 1.04677
myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] Subtracted 6711.27 6974.49 263.22
2250 esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Divided 6834.03 7153.66 1.04677
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Subtracted 6707.29 6970.07 262.78
2251 hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]
serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] Divided 6196.65 6486.12 1.04671
2252 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 5840.54 6113.01 1.04665
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] Subtracted 4806.38 5067 260.62
2253 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 4806.33 5066.92 260.59
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Divided 3629.21 3467.48 1.04664
2254 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 7383.13 7727.39 1.04663

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/