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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
description Rank Gene Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
description
Rank
Filtered
green
red
network_comparison
28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 407 1 260.544 239.75 1.08673
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193] 3147 0.00001 0.00001 1
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 299 0 11512.3 12338.7 1.07178
2756 1 0.00001 0.00001 1
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
3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] 2303 192.542 191.567 1.00509
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 0.00001 0.00001 1
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] 2189 208.162 209.54 1.00662
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 327 0 10466.5 9897.29 1.05751
1852 1 198.154 196.008 1.01095
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 478 0 10243.1 10156.4 1.00854
2300 1 192.541 191.563 1.00511
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 1025 199.266 205.632 1.03195
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] 1083 213.685 220.118 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] 1084
3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] 897 283.472 272.878 1.03882
38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] 2358 197.346 198.181 1.00423
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] 369 0 19704.7 18849.7 1.04536
1745 1 222.215 219.423 1.01272
40s ribosomal protein s11. [swissprot;acc:p04643] 278 267.088 241.399 1.10642
40s ribosomal protein s13. [swissprot;acc:q02546] 1722 223.813 220.899 1.01319
40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 386 264.11 242.238 1.09029
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 222 0 11013.2 12183 1.10622
304 1 266.986 242.339 1.1017
40s ribosomal protein s15a. [swissprot;acc:p39027] 292 266.414 241.411 1.10357
40s ribosomal protein s16. [swissprot;acc:p17008] 391 263.62 241.828 1.09011
40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 387 264.11 242.238 1.09029
40s ribosomal protein s19. [swissprot;acc:p39019] 861 224.958 234.025 1.04031
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 186 0 10592.8 11935.1 1.12672
344 1 265.136 241.625 1.0973
40s ribosomal protein s20. [swissprot;acc:p17075] 342 267.21 243.5 1.09737
40s ribosomal protein s21. [swissprot;acc:p35265] 790 234.511 224.244 1.04578
40s ribosomal protein s23. [swissprot;acc:p39028] 324 268.195 243.944 1.09941
40s ribosomal protein s24 (s19). [swissprot;acc:p16632] 1690 227.184 224.091 1.0138
40s ribosomal protein s26. [swissprot;acc:p02383] 112 0 17098 14269.7 1.1982
454 1 226.578 210.224 1.07779
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 380 0 9936.37 9566.15 1.0387
1102 1 235.974 229.442 1.02847
40s ribosomal protein s28. [swissprot;acc:p25112] 258 0 14193.6 12967.1 1.09459
1982 1 198.427 200.343 1.00966
40s ribosomal protein s29. [swissprot;acc:p30054] 225 0 9997.71 11035.3 1.10378
277 1 267.642 241.849 1.10665
40s ribosomal protein s3. [swissprot;acc:p23396] 346 265.119 241.612 1.09729
40s ribosomal protein s30. [swissprot;acc:q05472] 1081 216.875 223.44 1.03027
40s ribosomal protein s3a. [swissprot;acc:p49241] 331 0 10992.4 10405.1 1.05644
867 1 234.674 225.689 1.03981
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 261 0 11393.9 12448.9 1.09259
288 1 266.078 240.758 1.10517
40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 260 0 11392.6 12447.6 1.0926
287 1 266.079 240.758 1.10517

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/