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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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
green
red
network_comparison
57 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Measured Divided 2664.55 1631.67 1.63302
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Squared 129762 219048 1.68808
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Rooted Subtracted 120.823 137.446 16.623
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Ranked 245.247 185.678 59.569
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 Divided 28.9554 41.6879 1.43973
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Measured Subtracted 24908.5 20911 3997.5
58 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Ranked 245.247 185.678 59.569
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Divided 336.191 266.863 1.25979
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Measured 2664.55 1631.67 1.63302
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared 129762 219048 1.68808
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Rooted Subtracted 120.823 137.446 16.623
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided 28.9696 41.6969 1.43933
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Measured Subtracted 24908.5 20911 3997.5
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Squared 242989 173408 69581
59 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Measured 24908.5 20911 3997.5
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Ranked Divided 336.19 266.863 1.25978
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared 129762 219048 1.68808
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Measured 2664.55 1631.67 1.63302
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Rooted Subtracted 120.823 137.446 16.623
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] Divided 52.2064 37.2205 1.40262
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Ranked Subtracted 327.709 269.278 58.431
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared 130021 199594 69573
60 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Measured Divided 2765.82 4489.19 1.6231
cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Ranked Subtracted 327.655 269.254 58.401
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Divided 336.184 266.864 1.25976
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Squared 129762 219048 1.68808
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Rooted Subtracted 120.823 137.446 16.623
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared 126167 192904 66737
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 Divided 49.8119 35.6294 1.39806
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Measured Subtracted 12889.1 16771.5 3882.4
61 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 10307.5 6475.5 3832
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Divided 2765.82 4489.19 1.6231
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Ranked 336.182 266.864 1.25975
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Rooted 31.7159 43.4291 1.36932
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Subtracted 120.823 137.446 16.623
necdin. [swissprot;acc:q99608] Squared Divided 129762 219048 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] Ranked Subtracted 327.642 269.248 58.394
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Squared 126095 192779 66684
62 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Measured 10307.5 6475.5 3832
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Divided 2765.82 4489.19 1.6231
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Ranked 336.181 266.865 1.25974
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Rooted Subtracted 120.823 137.446 16.623
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Squared Divided 129762 219048 1.68808
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Rooted 31.7522 43.4519 1.36847
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Ranked Subtracted 327.601 269.23 58.371
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Squared 124480 189976 65496
63 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Ranked Divided 336.178 266.865 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 31.7576 43.4554 1.36835
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Subtracted 120.823 137.446 16.623
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared Divided 129762 219048 1.68808

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/