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

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/