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 Network Comparison Type description Filtered Interaction Map Value Type green red network_comparison
Results: HTML CSV LaTeX Showing element 401 to 450 of 38536 in total
Network Comparison Type  : Divided
Rank
description
Filtered
Interaction Map
Value Type
green
red
network_comparison
26 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] 0 High confidence Squared 0.344399 44.3683 128.828
Rooted 3.80565 13.7805 3.62106
cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Low confidence 22.2036 12.4097 1.78921
cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] 1 Ranked 238.454 286.347 1.20085
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] 0 High confidence 7533.33 12128.3 1.60995
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Measured 662 153 4.3268
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Low confidence Ranked 6526.57 9282.29 1.42223
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Measured 47 143 3.04255
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 1 High confidence Rooted 24.2954 40.3362 1.66024
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Measured 892.67 1833.01 2.0534
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 0 Low confidence Squared 0.355148 3.41692 9.62112
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 1 High confidence 457.521 143.692 3.18404
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Ranked 44 58 1.31818
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] Low confidence Rooted 60.737 51.3588 1.1826
sperm associated antigen 7. [refseq;acc:nm_004890] Measured 19280.8 23318 1.20939
vasodilator-stimulated phosphoprotein (vasp). [swissprot;acc:p50552] Squared 72915.2 97360.9 1.33526
27 camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] 0 Ranked 18516 13109 1.41246
cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] 1 237.743 284.798 1.19792
dystrophin. [swissprot;acc:p11532] 0 High confidence Rooted 5.12693 17.8026 3.47237
ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08] 1 Low confidence Squared 72915.2 97360.9 1.33526
glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] Rooted 45.0567 52.3425 1.1617
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] High confidence Measured 895.134 1834.33 2.04922
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Rooted 24.2968 40.3364 1.66015
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 0 Low confidence Measured 35.5 105.5 2.97183
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Squared 0.355148 3.41692 9.62112
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 1 High confidence Ranked 44 58 1.31818
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Squared 457.521 143.692 3.18404
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 0 Measured 139 570 4.10072
pnas-129. [sptrembl;acc:q9bxv8] Low confidence Rooted 9.246 16.4276 1.77673
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 1 Measured 4614.87 3840.85 1.20152
ptd016 protein. [refseq;acc:nm_016125] 0 High confidence Ranked 11234 18050 1.60673
syntaxin 10 (syn10). [swissprot;acc:o60499] Squared 0.109658 4.29982 39.2112
28 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 1 Low confidence Ranked 170 142 1.19718
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 0 High confidence Measured 139 570 4.10072
cab2. [refseq;acc:nm_033419] Low confidence Rooted 9.26646 5.30308 1.74737
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 1 High confidence Ranked 153.671 201.949 1.31416
elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9] 0 Low confidence 11505 16116.4 1.40082
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 1 Rooted 45.0567 52.3425 1.1617
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] High confidence 24.3043 40.3372 1.65967
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Measured 895.194 1834.36 2.04912
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Low confidence Squared 61881.5 82347.8 1.33073
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 0 0.355148 3.41692 9.62112
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Measured 35.5 105.5 2.97183
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 1 High confidence Squared 457.521 143.692 3.18404
p28 ing5. [refseq;acc:nm_032329] 0 Ranked 7562.05 12124.8 1.60337
ptd016 protein. [refseq;acc:nm_016125] Squared 5.90864 0.213018 27.7377
syntaxin 10 (syn10). [swissprot;acc:o60499] Rooted 3.64637 9.62443 2.63946
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1 Low confidence Measured 3719.66 3098.94 1.2003
29 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] High confidence Squared 457.521 143.692 3.18404
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Low confidence Ranked 170.557 203.115 1.19089

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/