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.


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 [...,...].
Gene description Rank Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
description
Rank
Interaction Map
Filtered
red
green
network_comparison
28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] 1782 Low confidence 1 7861.76 8120.67 1.03293
1955 High confidence 5195.3 5510.67 1.0607
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 16 Low confidence 21185 28492 1.34491
115 High confidence
28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] 835 5623.18 6218.77 1.10592
3803 Low confidence 8064.23 8257.86 1.02401
28s ribosomal protein s18b, mitochondrial precursor (mrp-s18-b) (mrps18b) (mrp-s18-2) (ptd017 protein) (hspc183). [swissprot;acc:q9y676] 4972 7611.44 7632.4 1.00275
28s ribosomal protein s18c, mitochondrial precursor (mrp-s18-c) (mrps18c) (mrp-s18-1) (cgi-134). [swissprot;acc:q9y3d5] 2324 8037.13 8286.09 1.03098
28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] 1446 7704.75 7969.42 1.03435
2071 High confidence 6437.24 6797.24 1.05592
28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 2530 3880.5 3788.42 1.02431
3986 Low confidence 7621.65 7792.73 1.02245
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193] 3147 High confidence 0.00001 0.00001 1
3493 Low confidence 8082.12 8292.57 1.02604
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 492 High confidence 0 5038.33 5046.33 1.00159
822 Low confidence
2756 High confidence 1 0.00001 0.00001 1
3487 Low confidence 8082.12 8292.57 1.02604
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 High confidence 0.00001 0.00001 1
3489 Low confidence 8082.12 8292.57 1.02604
3'(2'), 5'-bisphosphate nucleotidase 1; bisphosphate 3'-nucleotidase; bpntase; pap-inositol-1,4-phosphatase. [refseq;acc:nm_006085] 4994 6922.79 6911.72 1.0016
3'-5' rna exonuclease; polynucleotide phosphorylase-like. [refseq;acc:nm_033109] 2310 7602.32 7838.4 1.03105
3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] 2302 High confidence 6946.6 7263.68 1.04565
3321 Low confidence 8023.42 8238.4 1.02679
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
3728 Low confidence 7900.62 8094.29 1.02451
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] 143 10696.6 11639.5 1.08815
2105 High confidence 6916.14 7295.24 1.05481
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 438 0 2925.57 2853.65 1.0252
581 Low confidence 2015.65 1932.95 1.04278
1660 1 7966.46 8232.52 1.0334
1898 High confidence 6885.11 7317.48 1.0628
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 346 0 1837.26 1721.76 1.06708
459 Low confidence 1616.87 1500.63 1.07746
2305 High confidence 1 6946.82 7263.87 1.04564
3780 Low confidence 8168.73 8366.35 1.02419
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 563 High confidence 5480.24 6222.04 1.13536
2218 Low confidence 8425.53 8689.87 1.03137
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] 1274 High confidence 5885 6371.14 1.08261
2082 Low confidence 7887.47 8138.17 1.03178
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] 1275 High confidence 5885 6371.14 1.08261
2090 Low confidence 7887.47 8138.17 1.03178
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] 2235 8107.73 8361.72 1.03133
3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] 2547 High confidence 3370.46 3444.18 1.02187
3553 Low confidence 7733.78 7932.5 1.0257
38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] 2261 High confidence 6486.84 6786.23 1.04615
3779 Low confidence 8396.92 8198.63 1.02419
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] 121 High confidence 0 19.6667 14.3333 1.3721
727 Low confidence 1 8443.4 8803.2 1.04261
815 0 3831.93 3822.12 1.00257

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/