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 Gene Rank Value Type Filtered Network Comparison Type green Interaction Map red network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
description
Rank
Filtered
green
Interaction Map
red
network_comparison
abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910] 1935 1 216.279 High confidence 218.43 1.00995
2521 197.494 Low confidence 201.076 1.01814
abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] 779 197.229 202.48 1.02662
1845 214.702 High confidence 217.077 1.01106
abl-philin 2. [refseq;acc:nm_032327] 389 0 17688 Low confidence 16315 1.08416
3025 1 199.029 202.348 1.01668
acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] 2259 196.214 199.914 1.01886
2306 192.544 High confidence 191.571 1.00508
acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 2143 193.896 Low confidence 197.608 1.01914
2319 195.8 High confidence 194.842 1.00492
acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] 2144 193.891 Low confidence 197.602 1.01914
2315 195.787 High confidence 194.825 1.00494
acetyl-coenzyme a acetyltransferase 2; acetoacetyl coenzyme a thiolase. [refseq;acc:nm_005891] 4559 200.117 Low confidence 201.714 1.00798
acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] 2039 192.191 High confidence 190.551 1.00861
2376 196.211 Low confidence 199.85 1.01855
acetyl-coenzyme a transporter. [refseq;acc:nm_004733] 2713 198.156 201.627 1.01752
acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] 1421 211.391 High confidence 207.076 1.02084
2275 199.972 Low confidence 203.735 1.01882
acid sphingomyelinase-like phosphodiesterase 3a (ec 3.1.4.-) (asm-like phosphodiesterase 3a) (fragment). [swissprot;acc:q92484] 2956 198.377 201.732 1.01691
acid sphingomyelinase-like phosphodiesterase 3b precursor (ec 3.1.4.-) (asm-like phosphodiesterase 3b). [swissprot;acc:q92485] 2960
acidic 82 kda protein mrna. [refseq;acc:nm_014597] 4677 201.278 202.475 1.00595
acidic leucine-rich nuclear phosphoprotein 32 family member a (potent heat-stable protein phosphatase 2a inhibitor i1pp2a) (hla-dr associated protein i) (phapi) (acidic nuclear phosphoprotein pp32) (cerebellar leucine rich acidic nuclear protein). [swissprot;acc:p39687] 569 200.275 206.46 1.03088
acidic leucine-rich nuclear phosphoprotein 32 family member b (phapi2 protein) (silver-stainable protein ssp29) (acidic protein rich in leucines). [swissprot;acc:q92688] 572
acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423] 270 0 15399 17542 1.13916
567 1 200.275 206.46 1.03088
acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626] 271 0 15399 17542 1.13916
570 1 200.275 206.46 1.03088
aconitate hydratase, mitochondrial precursor (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:q99798] 1299 195.959 200.342 1.02237
acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 21 0 10621.4 High confidence 6313.38 1.68236
322 11238.6 Low confidence 10129.7 1.10947
2101 1 213.27 High confidence 211.71 1.00737
2308 197.572 Low confidence 201.265 1.01869
actin binding lim protein 2. [refseq;acc:nm_032432] 660 216.576 High confidence 229.072 1.0577
820 203.181 Low confidence 208.488 1.02612
actin, alpha cardiac. [swissprot;acc:p04270] 3962 198.479 200.879 1.01209
actin, aortic smooth muscle (alpha-actin 2). [swissprot;acc:p03996] 668 0 11418.9 11170.2 1.02226
3964 1 198.477 200.877 1.01209
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] 382 0 10061.8 High confidence 10449 1.03848
829 11085.2 Low confidence 11101.7 1.00149
1529 1 213.031 High confidence 216.762 1.01751
3630 197.828 Low confidence 200.633 1.01418
actin, gamma-enteric smooth muscle (alpha-actin 3). [swissprot;acc:p12718] 3961 198.477 200.877 1.01209
actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] 668 216.576 High confidence 229.072 1.0577
822 203.181 Low confidence 208.488 1.02612
actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142] 2626 225.195 High confidence 224.891 1.00135
3653 198.345 Low confidence 201.127 1.01403
actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391] 426 198.528 205.501 1.03512
2631 225.195 High confidence 224.891 1.00135
actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747] 727 196.189 Low confidence 201.571 1.02743
2634 225.195 High confidence 224.891 1.00135

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/