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 [...,...].
Value Type Rank Gene description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6036 to 6085 of 29840 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2516 eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] Divided 6203.95 6360.24 1.02519
2517 activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] Subtracted 3669.33 3797.78 128.45
eh-domain containing protein 2. [swissprot;acc:q9nzn4] Divided 6203.96 6360.24 1.02519
2518 chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185] Subtracted 7550.12 7422.01 128.11
sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422] Divided 6204.15 6360.27 1.02516
2519 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 5964.17 6113.96 1.02511
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Subtracted 3754.39 3629.51 124.88
2520 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 3708.67 3584.47 124.2
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] Divided 5964.17 6113.96 1.02511
2521 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]
40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Subtracted 3708.67 3584.47 124.2
2522 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 7181.3 7057.99 123.31
retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] Divided 5964.17 6113.96 1.02511
2523 dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 3803.04 3710.01 1.02508
skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] Subtracted 3634.59 3756.67 122.08
2524 myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] Divided 8695.15 8912.98 1.02505
skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192] Subtracted 3633.14 3754.96 121.82
2525 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] Divided 8695.15 8912.98 1.02505
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Subtracted 7169.01 7047.98 121.03
2526 chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197] 7538.48 7417.58 120.9
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Divided 8695.15 8912.98 1.02505
2527 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Subtracted 3730.53 3611.05 119.48
large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] Divided 8695.15 8912.98 1.02505
2528 40s ribosomal protein s16. [swissprot;acc:p17008] Subtracted 3730.53 3611.05 119.48
reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3] Divided 6205.14 6359.44 1.02487
2529 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Subtracted 3730.74 3611.45 119.29
protein cgi-147. [swissprot;acc:q9y3e5] Divided 6436.43 6283 1.02442
2530 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 3880.5 3788.42 1.02431
60s ribosomal protein l15. [swissprot;acc:p39030] Subtracted 4888.72 5006.1 117.38
2531 lim/homeobox protein lhx3. [swissprot;acc:q9ubr4] 7571.73 7688.39 116.66
polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] Divided 6141.97 6291.08 1.02428
2532 60s ribosomal protein l15. [swissprot;acc:p39030] 4888.72 5006.1 1.02401
lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290] Subtracted 7572.69 7689.04 116.35
2533 dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Divided 3847.84 3759.28 1.02356
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Subtracted 7572.7 7689.04 116.34
2534 lim/homeobox protein lhx4. [swissprot;acc:q969g2] 7573.83 7689.81 115.98
thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Divided 6452.33 6603.94 1.0235
2535 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957]
rad50 homolog isoform 1. [refseq;acc:nm_005732] Subtracted 7222.12 7110.74 111.38
2536 insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663] 7424.26 7534.05 109.79
sorting nexin 1. [swissprot;acc:q13596] Divided 5932.05 6071.35 1.02348
2537 mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Subtracted 4243.44 4352.56 109.12
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Divided 6669.22 6824.41 1.02327
2538 estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659] 7121.07 7286.61 1.02325
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Subtracted 3573.66 3682.14 108.48
2539 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] 3626.38 3734.8 108.42
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] Divided 3805.17 3718.86 1.02321
2540 osteoclast stimulating factor 1. [swissprot;acc:q92882] Subtracted 4708.98 4817.39 108.41
pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] Divided 6672.69 6827.51 1.0232
2541 tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] 8542.13 8740.23 1.02319

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/