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 4386 to 4435 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2193 serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] Subtracted 5379.49 5660.18 280.69
2194 dna repair protein rad52 homolog. [swissprot;acc:p43351] Divided 5285.38 5034.86 1.04976
neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] Subtracted 5379.33 5660 280.67
2195 abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910] 5864.49 6145.14 280.65
ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] Divided 6197.11 6504.93 1.04967
2196 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] 6688.64 7020.02 1.04954
quaking isoform 6. [sptrembl;acc:q9p0x9] Subtracted 5864.49 6145.14 280.65
2197 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Divided 5285.79 5036.39 1.04952
tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] Subtracted 5379.03 5659.64 280.61
2198 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] 5902.26 6181.21 278.95
complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021] Divided 6344.31 6657.98 1.04944
2199 sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238]
sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] Subtracted 5902.27 6181.21 278.94
2200 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711]
rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Divided 5076.73 5326.29 1.04916
2201 cytochrome c. [swissprot;acc:p00001]
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Subtracted 5902.27 6181.21 278.94
2202 heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Divided 5076.73 5326.29 1.04916
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Subtracted 5902.27 6181.21 278.94
2203 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 4813.13 5091.36 278.23
heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] Divided 5076.73 5326.29 1.04916
2204 fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306]
glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211] Subtracted 6066.61 6344.65 278.04
2205 rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062] 5819.36 6092.93 273.57
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] Divided 5076.73 5326.29 1.04916
2206 elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]
signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624] Subtracted 5833.01 6106.48 273.47
2207 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 5776.96 6049.61 272.65
rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] Divided 5076.73 5326.29 1.04916
2208 gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915] Subtracted 5776.96 6049.61 272.65
visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235] Divided 5259.97 5518.26 1.0491
2209 inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] Subtracted 5776.96 6049.61 272.65
neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076] Divided 5259.1 5517.22 1.04908
2210 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] Subtracted 5840.54 6113.01 272.47
neurocalcin delta. [swissprot;acc:p29554] Divided 5258.96 5517.06 1.04908
2211 40s ribosomal protein s20. [swissprot;acc:p17075] 3590.56 3422.6 1.04907
m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Subtracted 4450.17 4721.37 271.2
2212 homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] 8751.01 8480.03 270.98
thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [refseq;acc:nm_030755] Divided 6087.68 6385.84 1.04898
2213 c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] Subtracted 4860.34 5127.3 266.96
proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [swissprot;acc:p20618] Divided 6642.32 6967.61 1.04897
2214 chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] 5910.12 6199.28 1.04893
cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] Subtracted 6956.32 7223.14 266.82
2215 alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443]
kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Divided 5910.12 6199.28 1.04893
2216 conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746]
fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Subtracted 7243.19 7509.81 266.62
2217 fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114]
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Divided 5910.12 6199.28 1.04893
2218 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Subtracted 7355.46 7088.93 266.53

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/