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 4808 to 4857 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2404 oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055] Subtracted 218.2 218.984 0.784
2405 thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472] Divided 221.677 222.489 1.00366
upf0183 protein. [swissprot;acc:q9bsu1] Subtracted 218.2 218.984 0.784
2406 antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Divided 182.563 183.232 1.00366
2407 proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] 214.234 213.456 1.00364
translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] Subtracted 218.2 218.984 0.784
2408 dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Divided 194.407 193.706 1.00362
squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508] Subtracted 218.2 218.984 0.784
2409 lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760] Divided 194.407 193.706 1.00362
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] Subtracted 218.2 218.984 0.784
2410 lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330] Divided 194.407 193.706 1.00362
proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] Subtracted 214.234 213.456 0.778
2411 epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333] 217.873 218.644 0.771
mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Divided 194.407 193.706 1.00362
2412 lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260]
mesoderm induction early response 1. [refseq;acc:nm_020948] Subtracted 212.374 211.618 0.756
2413 proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788]
serpin b12. [swissprot;acc:q96p63] Divided 218.2 218.984 1.00359
2414 guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774] Subtracted 219.361 220.116 0.755
megsin (tp55) (serpin b7). [swissprot;acc:o75635] Divided 218.2 218.984 1.00359
2415 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Subtracted 217.366 218.117 0.751
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Divided 218.2 218.984 1.00359
2416 oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055]
zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] Subtracted 217.366 218.117 0.751
2417 elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639]
upf0183 protein. [swissprot;acc:q9bsu1] Divided 218.2 218.984 1.00359
2418 antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]
apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] Subtracted 210.205 209.454 0.751
2419 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] 215.807 216.556 0.749
translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] Divided 218.2 218.984 1.00359
2420 proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] Subtracted 213.048 212.3 0.748
squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508] Divided 218.2 218.984 1.00359
2421 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] Subtracted 220.681 221.425 0.744
apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] Divided 210.205 209.454 1.00359
2422 methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Subtracted 213.021 212.286 0.735
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] Divided 218.2 218.984 1.00359
2423 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] Subtracted 217.645 218.376 0.731
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Divided 220.682 221.471 1.00358
2424 histone deacetylase 4 (hd4). [swissprot;acc:p56524] 221.472
proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789] Subtracted 214.049 213.323 0.726
2425 histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Divided 220.682 221.472 1.00358
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Subtracted 235.812 235.088 0.724
2426 mesoderm induction early response 1. [refseq;acc:nm_020948] Divided 212.374 211.618 1.00357
solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749] Subtracted 235.812 235.088 0.724
2427 farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [swissprot;acc:p14324]
proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] Divided 212.374 211.618 1.00357
2428 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 192.871 193.555 1.00355
protocadherin 15 precursor. [swissprot;acc:q96qu1] Subtracted 235.812 235.088 0.724
2429 esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Divided 192.871 193.555 1.00355

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/