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 [...,...].
Network Comparison Type Value Type Gene green description Rank network_comparison red Filtered Interaction Map
Results: HTML CSV LaTeX Showing element 2275 to 2324 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
green
description
Rank
network_comparison
red
220.267 serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [swissprot;acc:o14965] 2569 1.00164 219.907
serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [swissprot;acc:q96gd4] 2566
serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [swissprot;acc:q9uqb9] 2568
220.348 similar to trna synthetase class ii. [refseq;acc:nm_152268] 2714 1.00056 220.224
220.351 leng5 protein. [refseq;acc:nm_024075] 2260 1.00566 221.599
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] 2262
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] 2264
tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] 2261
tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] 2263
220.363 exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] 1497 1.01866 224.476
220.371 kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] 2253 1.00604 219.047
220.377 kinesin-like protein kif3c. [swissprot;acc:o14782] 2248 1.00608 219.045
220.386 myosin viia. [swissprot;acc:q13402] 2639 1.00123 220.658
ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459] 2641
ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [swissprot;acc:p23567] 2640
220.395 brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] 2713 1.00057 220.521
brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] 2711
hsgcn1 (fragment). [sptrembl;acc:q99736] 2712
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] 2709
importin 8; ran-binding protein 8. [refseq;acc:nm_006390] 2710
220.411 transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] 1499 1.01859 224.509
220.432 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] 1584 1.01633 216.891
220.53 afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] 1725 1.01311 217.676
alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5] 1726
inositol polyphosphate multikinase. [refseq;acc:nm_152230] 1724
220.579 loh1cr12. [refseq;acc:nm_058169] 827 1.0431 230.087
unr protein. [swissprot;acc:o75534] 828
220.685 methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] 2325 1.00473 221.728
220.751 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 651 1.05877 233.725
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] 649
220.8 ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230] 2204 1.00649 219.377
220.811 lamin a/c (70 kda lamin). [swissprot;acc:p02545] 2038 1.00864 218.92
220.812 centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] 2037 1.00865 218.919
centaurin beta 2 (cnt-b2). [swissprot;acc:q15057] 2035
centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] 2034
220.813 lamin b1. [swissprot;acc:p20700] 2036
220.826 n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] 2394 1.00379 221.662
220.847 immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] 1706 1.01358 223.846
serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172] 1705
220.887 heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900] 2735 1.00025 220.943
220.927 atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] 2727 1.00033 221.001
atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010] 2728
rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873] 2726
220.963 heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238] 2724 1.00041 221.053
221.116 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] 2721 1.00043 221.022
221.176 putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] 2020 1.00901 223.168
221.177 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] 1509 1.01795 225.148
beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] 1510
221.225 cab2. [refseq;acc:nm_033419] 769 1.04873 210.946
dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] 771

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/