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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3358 to 3407 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
840 Ranked mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] 198.781 190.66 1.04259
Squared keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] 31100.1 36086.4 1.16033
Rooted tbc1 domain family member 5. [swissprot;acc:q92609] 65.0565 69.1533 1.06297
841 Measured mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] 5786.67 6395.78 1.10526
Ranked peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] 198.781 190.66 1.04259
Squared keratin associated protein 1.5. [refseq;acc:nm_031957] 31100.2 36086.5 1.16033
Rooted tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] 65.0565 69.1533 1.06297
842 Measured loh1cr12. [refseq;acc:nm_058169] 5195.48 5741.63 1.10512
Ranked jm1 protein. [refseq;acc:nm_014008] 219.762 210.806 1.04248
Squared star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] 31100.1 36086.4 1.16033
Rooted vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] 65.0565 69.1533 1.06297
843 Measured unr protein. [swissprot;acc:o75534] 5195.48 5741.63 1.10512
Ranked trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] 218.521 227.796 1.04244
Squared keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] 31100.2 36086.5 1.16033
Rooted numb-like protein (numb-r). [swissprot;acc:q9y6r0] 65.0565 69.1533 1.06297
844 Measured preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] 6276.97 6934.8 1.1048
Ranked c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 178.033 170.82 1.04223
Squared keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] 31100.2 36086.5 1.16033
Rooted tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] 65.0565 69.1533 1.06297
845 Measured 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] 6276.97 6934.8 1.1048
Ranked u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] 228.599 219.399 1.04193
Squared star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] 31100.1 36086.4 1.16033
Rooted vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] 65.0565 69.1533 1.06297
846 Measured biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] 5607.43 6194.98 1.10478
Ranked methyltransferase like 2. [refseq;acc:nm_018396] 147.211 153.371 1.04184
Squared keratin associated protein 4.4. [refseq;acc:nm_032524] 31100.2 36086.5 1.16033
Rooted protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] 65.0565 69.1533 1.06297
847 Measured cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] 6776.85 7485.55 1.10458
Ranked cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] 147.211 153.371 1.04184
Squared alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 31100.1 36086.4 1.16033
Rooted wd-repeat protein bing4. [swissprot;acc:o15213] 51.7527 55.0117 1.06297
848 Measured 4066.56 4491.65 1.10453
Ranked fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 147.211 153.371 1.04184
Squared pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] 31100.1 36086.4 1.16033
Rooted protein bap28. [swissprot;acc:q9h583] 51.1817 54.4034 1.06295
849 Measured dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] 6194.15 6839.37 1.10417
Ranked proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] 147.211 153.371 1.04184
Squared integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] 31100.1 36086.4 1.16033
Rooted ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 124.41 117.043 1.06294
850 Measured propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] 6194.15 6839.37 1.10417
Ranked cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] 107.842 112.329 1.04161
Squared star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4] 31100.1 36086.4 1.16033
Rooted serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 124.41 117.043 1.06294
851 Measured casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 4307.12 4755.03 1.10399
Ranked trs85 homolog. [swissprot;acc:q9y2l5] 107.842 112.329 1.04161
Squared ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] 31100.1 36086.4 1.16033
Rooted probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 65.1512 69.252 1.06294
852 Measured casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 4307.12 4755.03 1.10399
Ranked hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 193.114 185.412 1.04154
Squared ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] 31100.1 36086.4 1.16033

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/