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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 197 to 246 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
network_comparison
green
50 ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Ranked 133 1.26667 105
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Squared 28994.2 1.69212 17134.8
KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Rooted 27.7254 1.58807 44.0299
NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Measured 779.167 1.78438 1390.33
51 KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Rooted 27.7254 1.58807 44.0299
NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 779.167 1.78438 1390.33
SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked 133 1.26667 105
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Squared 28994.2 1.69212 17134.8
52 AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Ranked 133 1.26667 105
CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Measured 779.167 1.78438 1390.33
NEURL neuralized-like. [refseq;acc:nm_004210] Rooted 27.9107 1.58239 44.1656
VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Squared 28994.2 1.69212 17134.8
53 CDK2AP1 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 1.78438 1390.33
CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared 28994.2 1.69212 17134.8
JUNB transcription factor jun-b. [swissprot;acc:p17275] Ranked 201.144 1.26611 158.868
NDUFS4 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 1.50369 46.4619
54 DTX2 deltex 2. [refseq;acc:nm_020892] Measured 1618.84 1.63814 2651.88
JUND transcription factor jun-d. [swissprot;acc:p17535] Ranked 200.941 1.26425 158.941
MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Squared 219048 1.68808 129762
UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Rooted 40.0958 1.46645 58.7986
55 DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured 1629.21 1.63399 2662.12
KCND2 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 1.44038 28.9323
MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Squared 219048 1.68808 129762
PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Ranked 320.927 1.26134 254.434
56 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 266.856 1.25998 336.233
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Squared 219048 1.68808 129762
CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Rooted 41.6851 1.43986 28.9509
PBK 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
57 GNG12 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
58 GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Ranked 266.863 1.25979 336.191
KCND1 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
59 no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Ranked 266.863 1.25978 336.19
KHDRBS2 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
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] Rooted 37.2205 1.40262 52.2064
60 GBE1 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
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 35.6294 1.39806 49.8119
61 GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Ranked 266.864 1.25975 336.182
KCNIP1 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
NDN necdin. [swissprot;acc:q99608] Squared 219048 1.68808 129762
PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Measured 4489.19 1.6231 2765.82
62 GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Ranked 266.865 1.25974 336.181
KCNIP4 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/