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 description Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 932 to 981 of 66312 in total
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
Interaction Map
red
network_comparison
green
59 no value mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Divided Squared Low confidence 92930 1.29425 71802.1
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Subtracted Rooted 55.7075 7.5767 63.2842
ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Measured High confidence 20911 3997.5 24908.5
FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Low confidence 6485.05 1116.76 7601.81
GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Divided Ranked High confidence 266.863 1.25978 336.19
KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Subtracted 269.278 58.431 327.709
KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided Measured 1631.67 1.63302 2664.55
MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Subtracted Rooted 137.446 16.623 120.823
MTUS1 mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Ranked Low confidence 221.902 21.119 200.783
NDUFA12 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 233.134 1.10875 210.267
Rooted High confidence 37.2205 1.40262 52.2064
PLAA phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] Subtracted Squared Low confidence 80538.1 16346.4 64191.7
PPP1CC serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] High confidence 199594 69573 130021
60 no value cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Divided Rooted Low confidence 59.2532 1.11478 66.0541
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Subtracted Measured High confidence 16771.5 3882.4 12889.1
C1GALT1 core1 udp-galactose:n-acetylgalactosamine-alpha-r beta 1,3-galac. [refseq;acc:nm_020156] Squared Low confidence 73677.6 16178.9 57498.7
CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Ranked High confidence 269.254 58.401 327.655
FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Divided Low confidence 202.793 1.10839 182.961
GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Measured High confidence 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
HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Measured Low confidence 15464.1 1.13635 17572.7
LENG4 malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] Subtracted Ranked 211 20.635 231.635
MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Divided Squared High confidence 219048 1.68808 129762
MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Subtracted Rooted 137.446 16.623 120.823
PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared 192904 66737 126167
PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Divided Low confidence 92930.5 1.29425 71802.4
SON 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 High confidence 35.6294 1.39806 49.8119
TEX28P2 testis-specific protein tex28. [swissprot;acc:o15482] Subtracted Low confidence 51.7058 7.4602 59.166
TP53I3 tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] Measured 11371 1108.2 12479.2
61 APBA1 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Ranked 229.144 20.341 208.803
ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Measured High confidence 6475.5 3832 10307.5
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Divided Ranked Low confidence 202.792 1.10831 182.974
GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] High confidence 266.864 1.25975 336.182
GOSR2 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] Subtracted Rooted Low confidence 51.7058 7.4602 59.166
HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Divided Measured 15464.1 1.13635 17572.7
JUND transcription factor jun-d. [swissprot;acc:p17535] Subtracted 6614.51 1065.74 7680.25
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] Ranked High confidence 269.248 58.394 327.642
KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Divided Rooted 43.4291 1.36932 31.7159
MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Subtracted 137.446 16.623 120.823
NCDN neurochondrin. [refseq;acc:nm_014284] Squared Low confidence 73677.6 16178.9 57498.7
NDN necdin. [swissprot;acc:q99608] Divided High confidence 219048 1.68808 129762
PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Subtracted 192779 66684 126095
PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Divided Low confidence 92920.4 1.29422 71796.4
PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Measured High confidence 4489.19 1.6231 2765.82
SMYD2 set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Rooted Low confidence 59.2532 1.11478 66.0541
62 no value melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Subtracted High confidence 137.446 16.623 120.823
ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Measured 6475.5 3832 10307.5
BACH1 transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] Rooted Low confidence 79.2778 7.4298 86.7076
BNC1 zinc finger protein basonuclin. [swissprot;acc:q01954] Squared 105225 15083.7 90141.3
FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Ranked 202.802 20.072 182.73

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/