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 description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 401 to 450 of 66312 in total
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
Interaction Map
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] Subtracted Rooted Low confidence 39.2301 52.5277 13.2976
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] Divided Ranked 286.347 238.454 1.20085
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Rooted High confidence 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
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Subtracted 23693.7 18263 5430.7
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Squared 219048 129762 89286
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Low confidence 78998 57169.1 21828.9
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Rooted High confidence 146.94 167.046 20.106
n33 protein. [swissprot;acc:q13454] Ranked Low confidence 198 163 35
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Divided Squared High confidence 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
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Subtracted 322 253 69
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured Low confidence 13203.5 15033.4 1829.9
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] Divided 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 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] Ranked 284.798 237.743 1.19792
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] Subtracted Rooted 39.2489 52.5401 13.2912
ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08] Divided Squared 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] Measured High confidence 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
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Subtracted Ranked 267.136 336.077 68.941
implantation-associated protein. [refseq;acc:nm_032121] Low confidence 198 163 35
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Squared High confidence 219048 129762 89286
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Measured 23693.7 18263 5430.7
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Squared Low confidence 78977.2 57161.1 21816.1
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Measured 13470.1 11654.4 1815.7
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Divided Ranked High confidence 58 44 1.31818
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Subtracted Rooted 146.94 167.046 20.106
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Divided Squared 143.692 457.521 3.18404
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Measured Low confidence 3840.85 4614.87 1.20152
28 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Ranked 142 170 1.19718
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] High confidence 201.949 153.671 1.31416
Subtracted Low confidence 203.115 170.557 32.558
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] Rooted 39.8493 52.9343 13.085
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Squared 93450 72115.4 21334.6
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Rooted High confidence 149.165 129.699 19.466
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Divided Low confidence 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
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Subtracted Ranked 267.136 336.077 68.941
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Divided Squared Low confidence 82347.8 61881.5 1.33073
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Subtracted High confidence 219048 129762 89286
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Measured Low confidence 13466.8 11652.4 1814.4
necdin. [swissprot;acc:q99608] High confidence 23693.7 18263 5430.7
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Divided Squared 143.692 457.521 3.18404
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Measured Low confidence 3098.94 3719.66 1.2003
29 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Subtracted Ranked 250.244 217.843 32.401
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Divided Squared High confidence 143.692 457.521 3.18404

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/