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.


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