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 208 to 257 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
52 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Squared 28994.2 17134.8 1.69212
53 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Measured 779.167 1390.33 1.78438
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Rooted 30.8986 46.4619 1.50369
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared 28994.2 17134.8 1.69212
transcription factor jun-b. [swissprot;acc:p17275] Ranked 201.144 158.868 1.26611
54 deltex 2. [refseq;acc:nm_020892] Measured 1618.84 2651.88 1.63814
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Squared 219048 129762 1.68808
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Rooted 40.0958 58.7986 1.46645
transcription factor jun-d. [swissprot;acc:p17535] Ranked 200.941 158.941 1.26425
55 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured 1629.21 2662.12 1.63399
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Squared 219048 129762 1.68808
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Rooted 41.6734 28.9323 1.44038
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Ranked 320.927 254.434 1.26134
56 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Rooted 41.6851 28.9509 1.43986
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Ranked 266.856 336.233 1.25998
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Squared 219048 129762 1.68808
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Measured 1631.67 2664.55 1.63302
57 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Ranked 266.856 336.233 1.25998
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Measured 1631.67 2664.55 1.63302
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Squared 219048 129762 1.68808
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Rooted 41.6879 28.9554 1.43973
58 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Ranked 266.863 336.191 1.25979
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Measured 1631.67 2664.55 1.63302
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared 219048 129762 1.68808
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Rooted 41.6969 28.9696 1.43933
59 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Ranked 266.863 336.19 1.25978
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared 219048 129762 1.68808
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Measured 1631.67 2664.55 1.63302
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] Rooted 37.2205 52.2064 1.40262
60 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Measured 4489.19 2765.82 1.6231
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Ranked 266.864 336.184 1.25976
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Squared 219048 129762 1.68808
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] Rooted 35.6294 49.8119 1.39806
61 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Measured 4489.19 2765.82 1.6231
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Ranked 266.864 336.182 1.25975
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Rooted 43.4291 31.7159 1.36932
necdin. [swissprot;acc:q99608] Squared 219048 129762 1.68808
62 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Measured 4489.19 2765.82 1.6231
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Ranked 266.865 336.181 1.25974
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Squared 219048 129762 1.68808
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Rooted 43.4519 31.7522 1.36847
63 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Ranked 266.865 336.178 1.25973
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] Rooted 43.4554 31.7576 1.36835
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared 219048 129762 1.68808
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Measured 4489.19 2765.82 1.6231
64 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Rooted 63.8686 47.2654 1.35128
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Measured 4489.19 2765.82 1.6231
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Ranked 266.868 336.159 1.25965
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Squared 219048 129762 1.68808
65 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Rooted 63.8686 47.2654 1.35128

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/