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 Network Comparison Type description Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 444 to 493 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Network Comparison Type
description
Value Type
red
network_comparison
green
56 HOXA5 Subtracted homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Squared 173408 69581 242989
MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Rooted 137.446 16.623 120.823
PBK Divided 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 1.63302 2664.55
PYGL Subtracted glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Ranked 185.678 59.569 245.247
RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Measured 20911 3997.5 24908.5
57 no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Squared 173408 69581 242989
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Rooted 137.446 16.623 120.823
GNG12 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Ranked 266.856 1.25998 336.233
KCND3 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 1.43973 28.9554
KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Measured 1631.67 1.63302 2664.55
MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Squared 219048 1.68808 129762
MYO15A Subtracted myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Ranked 185.678 59.569 245.247
RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Measured 20911 3997.5 24908.5
58 GNG4 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Ranked 266.863 1.25979 336.191
HSD17B14 Subtracted retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Squared 173408 69581 242989
KCND1 Divided 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 1.43933 28.9696
KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Measured 1631.67 1.63302 2664.55
MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared 219048 1.68808 129762
MAGEA9 Subtracted melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Rooted 137.446 16.623 120.823
PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Ranked 185.678 59.569 245.247
RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Measured 20911 3997.5 24908.5
59 no value Divided hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared 219048 1.68808 129762
ANLN Subtracted anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Measured 20911 3997.5 24908.5
GNG3 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Ranked 266.863 1.25978 336.19
KCND2 Subtracted potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 269.278 58.431 327.709
KHDRBS2 Divided kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Measured 1631.67 1.63302 2664.55
MAGEA8 Subtracted melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Rooted 137.446 16.623 120.823
NDUFA12 Divided 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 1.40262 52.2064
PPP1CC Subtracted serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared 199594 69573 130021
60 no value ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Measured 16771.5 3882.4 12889.1
CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Ranked 269.254 58.401 327.655
GBE1 Divided 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Measured 4489.19 1.6231 2765.82
GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Ranked 266.864 1.25976 336.184
MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Squared 219048 1.68808 129762
MAGEC1 Subtracted melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Rooted 137.446 16.623 120.823
PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared 192904 66737 126167
SON Divided 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 1.39806 49.8119
61 ARRB2 Subtracted beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Measured 6475.5 3832 10307.5
GNG5 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Ranked 266.864 1.25975 336.182
KCND3 Subtracted 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] 269.248 58.394 327.642
KCNIP1 Divided kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Rooted 43.4291 1.36932 31.7159
MAGEA4 Subtracted melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 137.446 16.623 120.823
NDN Divided necdin. [swissprot;acc:q99608] Squared 219048 1.68808 129762
PPP1R2P9 Subtracted type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 192779 66684 126095
PYGB Divided glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Measured 4489.19 1.6231 2765.82
62 no value Subtracted melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Rooted 137.446 16.623 120.823
ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Measured 6475.5 3832 10307.5
GNG10 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Ranked 266.865 1.25974 336.181
KCND1 Subtracted potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 269.23 58.371 327.601
KCNIP4 Divided potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Rooted 43.4519 1.36847 31.7522

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/