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