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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 227 to 276 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
57 KHDRBS3 Measured kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 1631.67 2664.55 1.63302
MAGEA11 Squared melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 219048 129762 1.68808
58 GNG4 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 266.863 336.191 1.25979
KCND1 Rooted potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 41.6969 28.9696 1.43933
KHDRBS1 Measured kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1631.67 2664.55 1.63302
MAGEA2B Squared melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 219048 129762 1.68808
59 no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
GNG3 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 266.863 336.19 1.25978
KHDRBS2 Measured kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 1631.67 2664.55 1.63302
NDUFA12 Rooted nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 37.2205 52.2064 1.40262
60 GBE1 Measured 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 4489.19 2765.82 1.6231
GNG8 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 266.864 336.184 1.25976
MAGEA6 Squared melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 219048 129762 1.68808
SON Rooted son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] 35.6294 49.8119 1.39806
61 GNG5 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 266.864 336.182 1.25975
KCNIP1 Rooted kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] 43.4291 31.7159 1.36932
NDN Squared necdin. [swissprot;acc:q99608] 219048 129762 1.68808
PYGB Measured glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 4489.19 2765.82 1.6231
62 GNG10 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 266.865 336.181 1.25974
KCNIP4 Rooted potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 43.4519 31.7522 1.36847
MAGED1 Squared melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 219048 129762 1.68808
PYGL Measured glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 4489.19 2765.82 1.6231
63 no value Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 266.865 336.178 1.25973
KCNIP2 Rooted kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 43.4554 31.7576 1.36835
MAGEF1 Squared melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 219048 129762 1.68808
MYO15A Measured myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 4489.19 2765.82 1.6231
64 GBE1 Rooted 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 63.8686 47.2654 1.35128
GNG11 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 266.868 336.159 1.25965
MAGEB6B Squared melanoma antigen, family b, 6. [refseq;acc:nm_173523] 219048 129762 1.68808
PYGM Measured glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 4489.19 2765.82 1.6231
65 no value Squared melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 219048 129762 1.68808
GNAQ Ranked guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 267.136 336.077 1.25807
NEURL Measured neuralized-like. [refseq;acc:nm_004210] 1657.68 2690.25 1.6229
PYGB Rooted glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 63.8686 47.2654 1.35128
66 GNA11 Ranked guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 267.136 336.077 1.25807
MAGEA9 Squared melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 219048 129762 1.68808
NDUFA12 Measured nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 1991.03 3221.38 1.61795
PYGL Rooted glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 63.8686 47.2654 1.35128
67 ARRB2 Measured beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 6475.5 10307.5 1.59177
GNAT2 Ranked guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 267.14 336.075 1.25805
MAGEA8 Squared melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 219048 129762 1.68808
MYO15A Rooted myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 63.8686 47.2654 1.35128
68 ARRB1 Measured beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 6475.5 10307.5 1.59177
GNAZ Ranked guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 267.139 336.075 1.25805
MAGEC1 Squared melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 219048 129762 1.68808
PYGM Rooted glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 63.8686 47.2654 1.35128
69 GNAT1 Ranked guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 267.14 336.075 1.25805
MAGEA4 Squared melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 219048 129762 1.68808
NEUROD2 Rooted neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] 27.9136 37.2872 1.33581
SPATA6 Measured spermatogenesis associated 6. [refseq;acc:nm_019073] 6475.5 10307.5 1.59177

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
- Hugo is the HGNC identifier if it exists
- 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/