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 101 to 150 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
description
Rank
Network Comparison Type
Filtered
red
green
network_comparison
28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 340 Subtracted 1 239.75 260.544 20.794
407 Divided 1.08673
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193] 3147 0.00001 0.00001 1
Subtracted 0 0 0
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 284 0 12338.7 11512.3 826.4
299 Divided 1.07178
2756 1 0.00001 0.00001 1
Subtracted 0 0 0
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060] 2802 Divided 0.00001 0.00001 1
Subtracted 0 0 0
3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] 2303 Divided 191.567 192.542 1.00509
2333 Subtracted 0.975
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [swissprot;acc:q99714] 3180 Divided 0.00001 0.00001 1
Subtracted 0 0 0
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] 2189 Divided 209.54 208.162 1.00662
2201 Subtracted 1.378
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 327 Divided 0 9897.29 10466.5 1.05751
348 Subtracted 569.21
1852 Divided 1 196.008 198.154 1.01095
1914 Subtracted 2.146
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 473 0 10156.4 10243.1 86.7
478 Divided 1.00854
2300 1 191.563 192.541 1.00511
2331 Subtracted 0.978
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 1025 Divided 205.632 199.266 1.03195
1048 Subtracted 6.366
3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] 1040 220.118 213.685 6.433
1083 Divided 1.03011
3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] 1041 Subtracted 6.433
1084 Divided 1.03011
3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] 739 Subtracted 272.878 283.472 10.594
897 Divided 1.03882
38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] 2358 198.181 197.346 1.00423
2385 Subtracted 0.835
4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 277 0 18849.7 19704.7 855
369 Divided 1.04536
1720 Subtracted 1 219.423 222.215 2.792
1745 Divided 1.01272
40s ribosomal protein s11. [swissprot;acc:p04643] 199 Subtracted 241.399 267.088 25.689
278 Divided 1.10642
40s ribosomal protein s13. [swissprot;acc:q02546] 1695 Subtracted 220.899 223.813 2.914
1722 Divided 1.01319
40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 323 Subtracted 242.238 264.11 21.872
386 Divided 1.09029
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 205 Subtracted 0 12183 11013.2 1169.8
219 1 242.339 266.986 24.647
222 Divided 0 12183 11013.2 1.10622
304 1 242.339 266.986 1.1017
40s ribosomal protein s15a. [swissprot;acc:p39027] 206 Subtracted 241.411 266.414 25.003
292 Divided 1.10357

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/