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 327 to 376 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
82 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Divided 1 267.636 335.359 1.25304
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Subtracted 252.329 202.004 50.325
83 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 252.309 201.998 50.311
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Divided 88.2482 110.265 1.24949
small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678] 0 18359.8 14447.8 1.27077
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] Subtracted 18079 15652 2427
84 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Divided 1 88.2482 110.265 1.24949
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Subtracted 252.296 201.995 50.301
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Divided 0 12460.6 15781 1.26647
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Subtracted 12946.3 10519.7 2426.6
85 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Divided 1 88.2482 110.265 1.24949
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Subtracted 296.677 247.559 49.118
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Divided 0 9688.47 12104.2 1.24934
Subtracted 2415.73
86 alpha crystallin a chain. [swissprot;acc:p02489] 16372.4 13972.2 2400.2
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 1 335 286 49
high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] Divided 0 5677.96 4546.87 1.24876
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 1 88.2482 110.265 1.24949
87 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Subtracted 249.663 298.263 48.6
dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] Divided 0 5677.89 4547.43 1.24859
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Subtracted 16411.9 14027.1 2384.8
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Divided 1 88.2482 110.265 1.24949
88 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] 0 5677.86 4547.66 1.24852
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Subtracted 12787.8 10454.7 2333.1
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] 1 249.663 298.263 48.6
89 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] 0 12049 14370.7 2321.7
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Divided 1 88.2482 110.265 1.24949
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] 0 5677.58 4549.85 1.24786
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Subtracted 1 249.663 298.263 48.6
90 60s ribosomal protein l18a. [swissprot;acc:q02543] 0 12738.7 10437.1 2301.6
high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] Divided 5677.45 4550.87 1.24755
necdin. [swissprot;acc:q99608] 1 88.2482 110.265 1.24949
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Subtracted 249.663 298.263 48.6
91 bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] Divided 0 13841.2 11127.5 1.24387
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 1 88.2482 110.265 1.24949
suppressor of actin 1. [refseq;acc:nm_014016] Subtracted 0 19088.1 16804.6 2283.5
transcription factor lbx1. [swissprot;acc:p52954] 1 249.663 298.263 48.6
92 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 0 11545 13771.5 2226.5
dok-like protein. [refseq;acc:nm_024872] Divided 17571 21783 1.23971
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 1 88.2482 110.265 1.24949
mosaic protein lgn. [swissprot;acc:p81274] Subtracted 249.663 298.263 48.6
93 melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided 88.2482 110.265 1.24949
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 0 7739.47 9580.95 1.23793
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Subtracted 10585.3 12769.1 2183.8
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] 1 249.663 298.263 48.6
94 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 0 14222.5 12058.6 2163.9
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 1 88.2482 110.265 1.24949
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 0 12946.3 10519.7 1.23067

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/