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 3258 to 3307 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
815 p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44] Squared 21890.2 25445.6 1.16242
pbk1 protein. [sptrembl;acc:o76021] Rooted 51.7294 55.0405 1.06401
syntaxin 1b. [swissprot;acc:q15531] Ranked 212.386 221.785 1.04425
816 huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] Rooted 61.6699 65.6173 1.06401
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Ranked 212.386 221.785 1.04425
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Squared 26652.6 30968.4 1.16193
target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] Measured 5641.53 6256.17 1.10895
817 dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Ranked 212.386 221.785 1.04425
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Measured 6811.2 7547.35 1.10808
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Squared 44848.2 52108.3 1.16188
triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] Rooted 61.67 65.6173 1.06401
818 aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Measured 6807.78 7543.28 1.10804
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Rooted 125.493 117.944 1.064
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Ranked 168.592 161.452 1.04422
zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] Squared 44848.2 52108.3 1.16188
819 dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] Ranked 228.563 238.668 1.04421
ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Measured 6805.45 7540.5 1.10801
target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] Rooted 61.6715 65.6171 1.06398
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Squared 44848.2 52108.3 1.16188
820 mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Ranked 221.716 231.501 1.04413
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Measured 6805.86 7540.99 1.10801
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Rooted 125.447 117.906 1.06396
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Squared 23455.7 27251.7 1.16184
821 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] Rooted 61.3164 65.2371 1.06394
eif-5a2 protein. [refseq;acc:nm_020390] Squared 26472.2 30755.9 1.16182
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Measured 6257.99 6932.95 1.10786
u3 snornp protein 4 homolog. [refseq;acc:nm_033416] Ranked 221.676 231.453 1.0441
822 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Rooted 73.8577 78.5795 1.06393
eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Ranked 243.067 232.805 1.04408
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Measured 6311.6 6989.33 1.10738
ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781] Squared 27949.8 32471.7 1.16179
823 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Rooted 87.2414 92.8092 1.06382
immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] Squared 21317.5 24765.4 1.16174
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Measured 6311.83 6989.6 1.10738
transcription factor iib. [refseq;acc:nm_013242] Ranked 206.068 197.471 1.04354
824 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] Measured 5657.53 6263.02 1.10702
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Rooted 87.1967 92.7545 1.06374
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Squared 21095.7 24507.5 1.16173
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Ranked 206.068 197.471 1.04354
825 atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] Measured 5657.53 6263.02 1.10702
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Rooted 52.2412 49.113 1.06369
eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] Squared 26421.1 30691.2 1.16162
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Ranked 206.214 197.614 1.04352
826 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 223.186 213.912 1.04335
exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Measured 5195.58 5750.34 1.10678
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Rooted 62.9744 66.9825 1.06365
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Squared 21175.9 24598.1 1.16161
827 atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] 24211.7 28112.8 1.16112
loh1cr12. [refseq;acc:nm_058169] Ranked 230.087 220.579 1.0431
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Rooted 62.9744 66.9825 1.06365

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/