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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 458 to 507 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Value Type
Interaction Map
red
green
network_comparison
58 GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Ranked High confidence 266.863 336.191 1.25979
HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Measured Low confidence 15464.1 17572.7 1.13635
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 High confidence 41.6969 28.9696 1.43933
KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Measured 1631.67 2664.55 1.63302
MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared 219048 129762 1.68808
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 Low confidence 59.0909 66.1317 1.11915
PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Squared 93450 72115.4 1.29584
59 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Rooted 75.6323 67.6572 1.11788
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared High confidence 219048 129762 1.68808
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Measured Low confidence 15464.1 17572.7 1.13635
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] Squared 92930 71802.1 1.29425
GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Ranked High confidence 266.863 336.19 1.25978
KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Measured 1631.67 2664.55 1.63302
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] Ranked Low confidence 233.134 210.267 1.10875
Rooted High confidence 37.2205 52.2064 1.40262
60 no value cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Low confidence 59.2532 66.0541 1.11478
FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Ranked 202.793 182.961 1.10839
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 2765.82 1.6231
GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Ranked 266.864 336.184 1.25976
HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Measured Low confidence 15464.1 17572.7 1.13635
MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Squared High confidence 219048 129762 1.68808
PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Low confidence 92930.5 71802.4 1.29425
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 49.8119 1.39806
61 FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked Low confidence 202.792 182.974 1.10831
GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] High confidence 266.864 336.182 1.25975
HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Measured Low confidence 15464.1 17572.7 1.13635
KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Rooted High confidence 43.4291 31.7159 1.36932
NDN necdin. [swissprot;acc:q99608] Squared 219048 129762 1.68808
PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Low confidence 92920.4 71796.4 1.29422
PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Measured High confidence 4489.19 2765.82 1.6231
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 66.0541 1.11478
62 FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked 202.79 183.017 1.10804
GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] High confidence 266.865 336.181 1.25974
HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Measured Low confidence 15464.1 17572.7 1.13635
KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Rooted High confidence 43.4519 31.7522 1.36847
MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Squared 219048 129762 1.68808
PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Low confidence 92262.9 71400.2 1.29219
PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Measured High confidence 4489.19 2765.82 1.6231
SMYD1 set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Rooted Low confidence 59.2532 66.0541 1.11478
63 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Ranked High confidence 266.865 336.178 1.25973
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Measured Low confidence 15464.1 17572.7 1.13635
C1GALT1 core1 udp-galactose:n-acetylgalactosamine-alpha-r beta 1,3-galac. [refseq;acc:nm_020156] Squared 73677.6 57498.7 1.28138
KCNIP2 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 High confidence 43.4554 31.7576 1.36835
MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared 219048 129762 1.68808
MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Measured 4489.19 2765.82 1.6231
RBM7 putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Ranked Low confidence 265.688 239.902 1.10749
TBX19 t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Rooted 61.4851 68.1264 1.10801
64 GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 63.8686 47.2654 1.35128
GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Ranked 266.868 336.159 1.25965
HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Measured Low confidence 15464.1 17572.7 1.13635

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/