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 4408 to 4457 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2204 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
wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] Divided 6628.99 6952.04 1.04873
2219 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] 5853.67 6136.97 1.0484
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Subtracted 7355.46 7088.93 266.53
2220 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Divided 3936.2 3755.33 1.04816
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Subtracted 7355.46 7088.93 266.53
2221 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]
thrombospondin 3 precursor. [swissprot;acc:p49746] Divided 3936.33 3755.5 1.04815
2222 mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Subtracted 7355.46 7088.93 266.53
sqv-7-like protein (fragment). [sptrembl;acc:o95454] Divided 5309.65 5066.82 1.04793
2223 abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910] 5864.49 6145.14 1.04786
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Subtracted 7243.07 7509.58 266.51
2224 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 6956.62 7223.09 266.47
quaking isoform 6. [sptrembl;acc:q9p0x9] Divided 5864.49 6145.14 1.04786
2225 60s ribosomal protein l9. [swissprot;acc:p32969] 3750.99 3580.35 1.04766
fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] Subtracted 7242.75 7508.98 266.23
2226 eyes absent homolog 1. [swissprot;acc:q99502] 5785.08 6051.03 265.95
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Divided 3650.78 3484.91 1.0476
2227 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]
sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] Subtracted 5783.69 6048.87 265.18
2228 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Divided 3650.82 3484.97 1.04759
sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] Subtracted 5783.72 6048.9 265.18
2229 arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] 5783.76 6048.94

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/