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 description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
Interaction Map
green
red
network_comparison
63 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared High confidence 129762 219048 1.68808
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Measured 2765.82 4489.19 1.6231
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Ranked Low confidence 239.902 265.688 1.10749
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Rooted 68.1264 61.4851 1.10801
64 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 47.2654 63.8686 1.35128
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Measured 2765.82 4489.19 1.6231
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Ranked 336.159 266.868 1.25965
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Squared 129762 219048 1.68808
neurochondrin. [refseq;acc:nm_014284] Low confidence 57498.7 73677.6 1.28138
rab11-family interacting protein 4. [refseq;acc:nm_032932] Rooted 81.4944 73.6221 1.10693
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Measured 17572.7 15464.1 1.13635
transcription factor jun-d. [swissprot;acc:p17535] Ranked 183.361 202.709 1.10552
65 eferin. [swissprot;acc:o75154] Rooted 81.4944 73.6221 1.10693
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence 47.2654 63.8686 1.35128
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Ranked 336.077 267.136 1.25807
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Squared 129762 219048 1.68808
neuralized-like. [refseq;acc:nm_004210] Measured 2690.25 1657.68 1.6229
septin 6. [swissprot;acc:q14141] Low confidence 14773.7 13005.8 1.13593
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Squared 95493.3 75490.8 1.26497
transcription factor jun-b. [swissprot;acc:p17275] Ranked 183.388 202.728 1.10546
66 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Rooted 61.8016 55.8923 1.10573
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] High confidence 47.2654 63.8686 1.35128
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Ranked 336.077 267.136 1.25807
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Squared 129762 219048 1.68808
mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Ranked Low confidence 200.783 221.902 1.10518
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] Measured High confidence 3221.38 1991.03 1.61795
septin 10 isoform 1. [refseq;acc:nm_144710] Squared Low confidence 94281 74803.9 1.26038
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] Measured 5555.81 4900.7 1.13368
67 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] High confidence 10307.5 6475.5 1.59177
brachyury protein (t protein). [swissprot;acc:o15178] Rooted Low confidence 68.2003 61.687 1.10559
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked High confidence 336.075 267.14 1.25805
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Measured Low confidence 13781.8 12176.9 1.1318
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Squared High confidence 129762 219048 1.68808
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Rooted 47.2654 63.8686 1.35128
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Ranked Low confidence 149.799 165.535 1.10505
septin 6. [swissprot;acc:q14141] Squared 93531.9 74378.4 1.25751
68 60s ribosomal protein l37a. [swissprot;acc:p12751] Ranked 217.005 239.692 1.10455
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Measured High confidence 10307.5 6475.5 1.59177
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Rooted 47.2654 63.8686 1.35128
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Ranked 336.075 267.139 1.25805
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Squared 129762 219048 1.68808
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Measured Low confidence 17265.4 19498.1 1.12932
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Rooted 61.8641 55.9786 1.10514
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Squared 35068.7 27909.1 1.25653
69 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Measured 7848.45 6991.78 1.12253
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] Rooted 67.1136 60.7884 1.10405
delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [swissprot;acc:p30038] Squared 64191.7 80538.1 1.25465
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Ranked High confidence 336.075 267.14 1.25805
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Squared 129762 219048 1.68808
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Rooted 37.2872 27.9136 1.33581

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/