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

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/