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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description Rank Gene Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 401 to 450 of 3228 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
description
Rank
red
green
network_comparison
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 143 9275.1 7089.65 1.30826
beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] 1764 5829.61 6218.27 1.06667
beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] 1765
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 68 6475.5 10307.5 1.59177
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 67
beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] 1673 5791.14 6193.02 1.0694
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 1672
beta-catenin (pro2286). [swissprot;acc:p35222] 1029 5635.26 6166.09 1.0942
beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] 1152 5322.74 5793.15 1.08838
beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] 2718 5603.24 5583.64 1.00351
beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [swissprot;acc:q9ubr1] 3145 0.00001 0.00001 1
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] 1844 3591.95 3375.34 1.06417
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 1842
bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] 1209 5420.87 5887.53 1.08609
bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] 2462 5114.15 5272.92 1.03105
bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] 1980 5830.46 6176.71 1.05939
biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] 846 5607.43 6194.98 1.10478
block 23. [sptrembl;acc:q8nhw5] 2260 5150.14 5387.84 1.04615
block of proliferation 1. [swissprot;acc:q14137] 470 3796.24 4348.59 1.1455
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 2270 6568.41 6869.9 1.0459
2272 6568.51 6869.97 1.04589
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 2271
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 861 5734.15 6326.41 1.10329
bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] 2406 5078.5 5275.76 1.03884
bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003] 3069 0.00001 0.00001 1
bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004] 2896
bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075] 3128
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 2773
brachyury protein (t protein). [swissprot;acc:o15178] 1631 6179.59 6613.15 1.07016
brain protein 16. [refseq;acc:nm_016458] 1923 5774.02 6133.01 1.06217
brain protein 44. [swissprot;acc:o95563] 328 15999.1 19007.1 1.18801
branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 1213 5890.62 6396.53 1.08588
branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 1215 5892.05 6397.28 1.08575
brca1 associated protein. [refseq;acc:nm_006768] 3161 0.00001 0.00001 1
brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 1939 5669.9 6015.75 1.061
brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] 2116 3672.49 3482.34 1.0546
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 173 4579.34 5940.64 1.29727
breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 2442 5454.62 5637.88 1.0336
breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 418 5493.1 6350.19 1.15603
brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] 1425 5628.53 6063.61 1.0773
brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] 1423
brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 443 6252.27 7192.51 1.15038
bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4] 3149 0.00001 0.00001 1
bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] 1925 7260.23 7711.29 1.06213
bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696] 3139 0.00001 0.00001 1
bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 1892 5438.52 5783.01 1.06334
bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] 1891 5438.18 5782.62
bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] 1888 5438.6 5783.11 1.06335
bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7] 3214 0.00001 0.00001 1
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] 2664 4608.91 4576.78 1.00702

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/