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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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

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/