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 Network Comparison Type description Value Type green Filtered Interaction Map network_comparison red
Results: HTML CSV LaTeX Showing element 451 to 500 of 25824 in total
Filtered  : 1
Interaction Map  : High confidence
Rank
Network Comparison Type
description
Value Type
green
network_comparison
red
57 Divided melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Squared 129762 1.68808 219048
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 28.9554 1.43973 41.6879
Subtracted homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Squared 242989 69581 173408
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Rooted 120.823 16.623 137.446
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Ranked 245.247 59.569 185.678
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Measured 24908.5 3997.5 20911
58 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Ranked 336.191 1.25979 266.863
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Measured 2664.55 1.63302 1631.67
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared 129762 1.68808 219048
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Rooted 28.9696 1.43933 41.6969
Subtracted glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Ranked 245.247 59.569 185.678
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Rooted 120.823 16.623 137.446
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Measured 24908.5 3997.5 20911
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Squared 242989 69581 173408
59 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Ranked 336.19 1.25978 266.863
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared 129762 1.68808 219048
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Measured 2664.55 1.63302 1631.67
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 52.2064 1.40262 37.2205
Subtracted anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Measured 24908.5 3997.5 20911
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Rooted 120.823 16.623 137.446
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Ranked 327.709 58.431 269.278
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared 130021 69573 199594
60 Divided 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Measured 2765.82 1.6231 4489.19
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Ranked 336.184 1.25976 266.864
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Squared 129762 1.68808 219048
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 49.8119 1.39806 35.6294
Subtracted cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Ranked 327.655 58.401 269.254
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Rooted 120.823 16.623 137.446
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared 126167 66737 192904
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Measured 12889.1 3882.4 16771.5
61 Divided glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 2765.82 1.6231 4489.19
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Ranked 336.182 1.25975 266.864
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Rooted 31.7159 1.36932 43.4291
necdin. [swissprot;acc:q99608] Squared 129762 1.68808 219048
Subtracted beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Measured 10307.5 3832 6475.5
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Rooted 120.823 16.623 137.446
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 327.642 58.394 269.248
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Squared 126095 66684 192779
62 Divided glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Measured 2765.82 1.6231 4489.19
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Ranked 336.181 1.25974 266.865
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Squared 129762 1.68808 219048
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Rooted 31.7522 1.36847 43.4519
Subtracted beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Measured 10307.5 3832 6475.5
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Rooted 120.823 16.623 137.446
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Ranked 327.601 58.371 269.23
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Squared 124480 65496 189976
63 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Ranked 336.178 1.25973 266.865
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 1.36835 43.4554
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared 129762 1.68808 219048
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Measured 2765.82 1.6231 4489.19

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/