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