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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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 [...,...].
Gene description Value Type Network Comparison Type Rank Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
description
Rank
Filtered
Interaction Map
red
green
network_comparison
28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] 729 1 Low confidence 205.65 200.165 1.0274
2212 High confidence 224.411 225.854 1.00643
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 9 Low confidence 58 44 1.31818
23 High confidence
28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] 1659 217.925 214.826 1.01443
2664 Low confidence 201.194 197.699 1.01768
28s ribosomal protein s18b, mitochondrial precursor (mrp-s18-b) (mrps18b) (mrp-s18-2) (ptd017 protein) (hspc183). [swissprot;acc:q9y676] 3958 201.908 204.37 1.01219
28s ribosomal protein s18c, mitochondrial precursor (mrp-s18-c) (mrps18c) (mrp-s18-1) (cgi-134). [swissprot;acc:q9y3d5] 3329 200.825 197.742 1.01559
28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] 730 206.555 201.05 1.02738
2675 High confidence 214.893 215.108 1.001
28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 407 239.75 260.544 1.08673
4992 Low confidence 206.266 206.342 1.00037
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193] 1667 197.872 193.866 1.02066
3147 High confidence 0.00001 0.00001 1
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 299 0 12338.7 11512.3 1.07178
453 Low confidence
1663 1 197.872 193.866 1.02066
2756 High confidence 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] 1665 Low confidence 197.872 193.866 1.02066
2802 High confidence 0.00001 0.00001 1
3'(2'), 5'-bisphosphate nucleotidase 1; bisphosphate 3'-nucleotidase; bpntase; pap-inositol-1,4-phosphatase. [refseq;acc:nm_006085] 178 Low confidence 209.954 221.607 1.0555
3'-5' rna exonuclease; polynucleotide phosphorylase-like. [refseq;acc:nm_033109] 1373 206.13 201.696 1.02198
3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] 2303 High confidence 191.567 192.542 1.00509
3261 Low confidence 199.744 196.642 1.01577
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 High confidence 0.00001 0.00001 1
4091 Low confidence 202.282 200.093 1.01094
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] 1250 180.665 176.667 1.02263
2189 High confidence 209.54 208.162 1.00662
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 327 0 9897.29 10466.5 1.05751
501 Low confidence 10721.7 11352.1 1.0588
879 1 203.354 198.284 1.02557
1852 High confidence 196.008 198.154 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 10156.4 10243.1 1.00854
614 Low confidence 10641.4 10984.2 1.03221
2300 1 High confidence 191.563 192.541 1.00511
2649 Low confidence 195.904 192.486 1.01776
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 1025 High confidence 205.632 199.266 1.03195
2252 Low confidence 196.562 192.92 1.01888
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] 949 204.147 199.196 1.02485
1083 High confidence 220.118 213.685 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] 950 Low confidence 204.147 199.196 1.02485
1084 High confidence 220.118 213.685 1.03011
3-oxo-5-beta-steroid 4-dehydrogenase (ec 1.3.99.6) (delta(4)-3- ketosteroid 5-beta-reductase) (aldo-keto reductase family 1 member d1). [swissprot;acc:p51857] 1902 Low confidence 201.286 197.384 1.01977
3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] 897 High confidence 272.878 283.472 1.03882
4765 Low confidence 206.842 205.83 1.00492
38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] 2068 203.696 207.631 1.01932
2358 High confidence 198.181 197.346 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 18849.7 19704.7 1.04536
481 Low confidence 11454.3 10788.6 1.0617
1745 1 High confidence 219.423 222.215 1.01272

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/