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 951 to 1000 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
description
Rank
Network Comparison Type
Filtered
red
green
network_comparison
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 Divided 1 213.422 213.75 1.00154
2577 Subtracted 0.328
beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] 2578 Divided 1.00154
Subtracted 0.328
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 50 Divided 133 105 1.26667
164 Subtracted 28
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 49 Divided 1.26667
163 Subtracted 28
beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] 2178 221.509 220.108 1.401
2222 Divided 1.00637
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 30 0 7395 11625 1.57201
41 Subtracted 4230
2177 1 221.509 220.108 1.401
2221 Divided 1.00637
beta-catenin (pro2286). [swissprot;acc:p35222] 778 Subtracted 224.445 214.894 9.551
801 Divided 1.04445
beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] 1482 Subtracted 225.148 221.177 3.971
1510 Divided 1.01795
beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] 796 Subtracted 212.386 221.785 9.399
808 Divided 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
Subtracted 0 0 0
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] 193 241.373 267.352 25.979
273 Divided 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] 191 Subtracted 25.979
237 Divided 0 9984 9067 1.10114
262 Subtracted 917
271 Divided 1 241.373 267.352 1.10763
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
Subtracted 0.094
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] 685 223.58 235.027 11.447
740 Divided 1.0512
bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] 1836 Subtracted 218.441 216.064 2.377
1848 Divided 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] 1699 Subtracted 218.436 215.553 2.883
1711 Divided 1.01337
block 23. [sptrembl;acc:q8nhw5] 117 Subtracted 0 11469.3 13334.8 1865.5
149 Divided 1.16265
1021 Subtracted 1 226.205 232.858 6.653
1091 Divided 1.02941
block of proliferation 1. [swissprot;acc:q14137] 438 Subtracted 250.794 234.433 16.361
512 Divided 1.06979
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 363 Subtracted 0 16680.7 17180.3 499.6
365 16684 17183 499
418 Divided 16680.7 17180.3 1.02995
420 16684 17183 1.02991
1930 1 196.964 198.935 1.01001
1932 196.965 198.936
1987 Subtracted 196.964 198.935 1.971
1988 196.965 198.936

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/