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 3380 to 3429 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
845 vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Rooted 65.0565 69.1533 1.06297
846 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] Measured 5607.43 6194.98 1.10478
keratin associated protein 4.4. [refseq;acc:nm_032524] Squared 31100.2 36086.5 1.16033
methyltransferase like 2. [refseq;acc:nm_018396] Ranked 147.211 153.371 1.04184
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Rooted 65.0565 69.1533 1.06297
847 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Squared 31100.1 36086.4 1.16033
cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Ranked 147.211 153.371 1.04184
cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Measured 6776.85 7485.55 1.10458
wd-repeat protein bing4. [swissprot;acc:o15213] Rooted 51.7527 55.0117 1.06297
848 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Ranked 147.211 153.371 1.04184
pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] Squared 31100.1 36086.4 1.16033
protein bap28. [swissprot;acc:q9h583] Rooted 51.1817 54.4034 1.06295
wd-repeat protein bing4. [swissprot;acc:o15213] Measured 4066.56 4491.65 1.10453
849 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
integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] Squared 31100.1 36086.4 1.16033
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] Ranked 147.211 153.371 1.04184
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Rooted 124.41 117.043 1.06294
850 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] Ranked 107.842 112.329 1.04161
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] Measured 6194.15 6839.37 1.10417
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Rooted 124.41 117.043 1.06294
star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4] Squared 31100.1 36086.4 1.16033
851 casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Measured 4307.12 4755.03 1.10399
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Rooted 65.1512 69.252 1.06294
ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] Squared 31100.1 36086.4 1.16033
trs85 homolog. [swissprot;acc:q9y2l5] Ranked 107.842 112.329 1.04161
852 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Measured 4307.12 4755.03 1.10399
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Ranked 193.114 185.412 1.04154
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Rooted 58.5869 62.2732 1.06292
ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] Squared 31100.1 36086.4 1.16033
853 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Measured 4078.45 4502.32 1.10393
ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] Squared 31100.1 36086.4 1.16033
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Rooted 64.0287 68.0566 1.06291
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Ranked 108.289 112.772 1.0414
854 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Rooted 64.0316 68.0597 1.06291
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Squared 31100.2 36086.5 1.16033
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Measured 6562.98 7242.37 1.10352
855 ero1-like. [refseq;acc:nm_014584]
espin. [refseq;acc:nm_031475] Squared 31100.1 36086.4 1.16033
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Rooted 64.0262 68.0537 1.0629
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Ranked 178.514 171.42 1.04138
856 cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] Squared 31100.1 36086.4 1.16033
heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Measured 5210.58 5749.33 1.1034
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Rooted 58.5944 62.2766 1.06284
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Ranked 215.028 206.623 1.04068
857 mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Rooted 58.6002 62.2793 1.06278
n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Measured 5210.58 5749.33 1.1034
pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] Squared 31100.1 36086.4 1.16033
putatative 28 kda protein. [refseq;acc:nm_020143] Ranked 227.241 236.467 1.0406
858 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Rooted 65.1843 69.2736 1.06273

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/