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 Value Type Gene 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  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
description
Rank
red
green
network_comparison
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 301 150.982 166.372 1.10193
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] 2576 213.422 213.75 1.00154
beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] 2578
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 50 133 105 1.26667
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 49
beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] 2222 221.509 220.108 1.00637
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 2221
beta-catenin (pro2286). [swissprot;acc:p35222] 801 224.445 214.894 1.04445
beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] 1510 225.148 221.177 1.01795
beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] 808 212.386 221.785 1.04425
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] 273 241.373 267.352 1.10763
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] 271
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] 2721 221.022 221.116 1.00043
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] 740 223.58 235.027 1.0512
bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] 1848 218.441 216.064 1.011
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] 1711 218.436 215.553 1.01337
block 23. [sptrembl;acc:q8nhw5] 1091 226.205 232.858 1.02941
block of proliferation 1. [swissprot;acc:q14137] 512 250.794 234.433 1.06979
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 1930 196.964 198.935 1.01001
1932 196.965 198.936
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 1928 196.964 198.935
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 1748 215.673 212.971 1.01269
bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] 793 224.244 234.511 1.04578
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] 2040 210.586 208.803 1.00854
brain protein 16. [refseq;acc:nm_016458] 1847 216.811 219.195 1.011
brain protein 44. [swissprot;acc:o95563] 742 126.215 120.078 1.05111
branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 2672 210.957 210.741 1.00102
branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 2687 210.939 210.755 1.00087
brca1 associated protein. [refseq;acc:nm_006768] 3161 0.00001 0.00001 1
brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 1752 216.271 218.991 1.01258
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] 294 240.782 265.717 1.10356
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 229 226.401 202.094 1.12028
breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 939 216.501 224.27 1.03588
breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 691 217.602 206.195 1.05532
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] 2713 220.521 220.395 1.00057
brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] 2711
brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 945 212.44 205.085 1.03586
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] 2747 201.477 201.514 1.00018
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] 2241 222.96 224.338 1.00618
bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] 2237 222.965 224.343
bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] 2238 222.959 224.337
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] 449 228.463 246.33 1.07821

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/