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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5608 to 5657 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1402 udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] Squared 25427.4 28520.7 1.12165
1403 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] Rooted 68.5259 71.2383 1.03958
enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Ranked 184.656 180.823 1.0212
importin 4. [refseq;acc:nm_024658] Measured 5613.16 6050.16 1.07785
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] Squared 23178.4 25996.4 1.12158
1404 mesoderm induction early response 1. [refseq;acc:nm_020948] Measured 6291.89 6781.6 1.07783
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Rooted 100.26 96.4491 1.03951
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] Squared 19596.8 21975 1.12136
splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] Ranked 232.752 237.65 1.02104
1405 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] Squared 19596.4 21974.6 1.12136
eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] Ranked 245.532 240.483 1.021
proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] Measured 6291.89 6781.6 1.07783
ubiquitin. [swissprot;acc:p02248] Rooted 68.5562 71.2644 1.0395
1406 cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] 61.6284 64.0609 1.03947
dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] Squared 24597.4 27579 1.12122
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Ranked 212.833 208.456 1.021
ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477] Measured 6210.51 6693.49 1.07777
1407 lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] Rooted 61.0274 63.4251 1.03929
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Squared 29964.5 33596.3 1.1212
transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] Measured 5692.53 6134.64 1.07766
wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830] Ranked 206.104 210.424 1.02096
1408 dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] Squared 29964.5 33596.3 1.1212
lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055] Rooted 61.0274 63.4251 1.03929
serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] Measured 6268.94 6755.57 1.07763
stromal interaction molecule 1 precursor. [swissprot;acc:q13586] Ranked 206.102 210.42 1.02095
1409 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] Squared 21512.7 24115.7 1.121
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808] Measured 5358.19 5773.37 1.07749
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Rooted 65.3456 67.9119 1.03927
trap/mediator complex component trap25. [refseq;acc:nm_080651] Ranked 206.102 210.42 1.02095
1410 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] Measured 6274.62 6760.78 1.07748
heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] Rooted 65.3456 67.9119 1.03927
malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Squared 17102.5 19171.7 1.12099
wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] Ranked 206.1 210.417 1.02095
1411 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] Measured 5812.02 6262.07 1.07743
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Rooted 65.3456 67.9119 1.03927
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Squared 8107.35 9087.76 1.12093
serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013] Ranked 206.102 210.42 1.02095
1412 heat shock cognate 71 kda protein. [swissprot;acc:p11142] Rooted 65.3456 67.9119 1.03927
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Measured 5813.84 6263.92 1.07742
polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765] Ranked 206.102 210.42 1.02095
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] Squared 22981.1 25758.4 1.12085
1413 acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310] Ranked 206.102 210.42 1.02095
histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Measured 5813.88 6263.97 1.07742
homolog of yeast maf1. [refseq;acc:nm_032272] Rooted 65 67.552 1.03926
translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] Squared 22981.1 25758.4 1.12085
1414 histone deacetylase 4 (hd4). [swissprot;acc:p56524] Measured 5813.88 6263.96 1.07741
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Ranked 206.102 210.42 1.02095
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Rooted 65 67.552 1.03926
uridine kinase-like 1. [swissprot;acc:q9nwz5] Squared 24302 27238.6 1.12084
1415 14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312] Measured 5815.33 6265.44 1.0774

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/