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.


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 [...,...].
Rank Gene description green Filtered Value Type Interaction Map Network Comparison Type red network_comparison
Results: HTML CSV LaTeX Showing element 351 to 400 of 38536 in total
Network Comparison Type  : Divided
Rank
description
green
Filtered
Value Type
Interaction Map
red
network_comparison
22 similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 0.00001 0 Measured High confidence 60 6000000
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] 12.49 Rooted 3.16228 3.94968
23 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 44 1 Ranked 58 1.31818
carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267] 0.00001 0 Measured Low confidence 37 3700000
carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 32028.5 1 40899 1.27696
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 76.7316 Rooted 63.2736 1.2127
gbp protein isoform a. [refseq;acc:nm_017870] 1894.39 Measured High confidence 699.76 2.7072
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] 59 0 0.00001 5900000
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 24.2919 1 Rooted 40.3358 1.66046
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 9285.44 0 Ranked 15520.4 1.67148
implantation-associated protein. [refseq;acc:nm_032121] 163 1 Low confidence 198 1.21472
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 57169.1 Squared 78998 1.38183
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 0.796213 0 High confidence 174.646 219.346
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] 457.521 1 143.692 3.18404
protein kinase, lysine deficient 3. [refseq;acc:nm_020922] 21.7584 0 Rooted Low confidence 10.6742 2.03841
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] 3.87298 High confidence 1 3.87298
serpin b12. [swissprot;acc:q96p63] 21138.6 Ranked Low confidence 14604.2 1.44743
tenascin-x precursor (tn-x) (hexabrachion-like). [swissprot;acc:p22105] 351.167 Squared 31.7555 11.0585
24 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 4577.5 1 Measured 5720.25 1.24965
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 8257 0 Ranked High confidence 13730.5 1.66289
bcl2-related ovarian killer. [refseq;acc:nm_032515] 61.2591 1 Rooted Low confidence 50.6099 1.21042
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 11.7898 0 23.8747 2.02503
cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] 57.5264 Squared 5.61325 10.2483
493 Measured 154 3.2013
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 457.521 1 Squared High confidence 143.692 3.18404
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 0.02001 0 4.16226 208.009
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 24.2941 1 Rooted 40.336 1.66032
histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] 228.509 Ranked Low confidence 188.298 1.21355
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 21113.7 0 14592 1.44694
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 57161.1 1 Squared 78977.2 1.38166
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 7.61577 0 Rooted High confidence 29.3087 3.84842
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 44 1 Ranked 58 1.31818
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 2108.52 Measured 950.561 2.21818
ptd016 protein. [refseq;acc:nm_016125] 158 0 30 5.26667
25 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] 238.476 1 Ranked Low confidence 286.396 1.20094
60s ribosomal protein l37a. [swissprot;acc:p12751] 0.344399 0 Squared High confidence 44.3683 128.828
3.80565 Rooted 13.7805 3.62106
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 56522.1 1 Squared Low confidence 77316.3 1.3679
doc-1 related protein (doc-1r). [swissprot;acc:o75956] 457.521 High confidence 143.692 3.18404
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 24.295 Rooted 40.3361 1.66026
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 892.67 Measured 1833.01 2.0534
histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] 56.875 Rooted Low confidence 67.7094 1.19049
4691.96 Measured 5847.46 1.24627
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 39.8063 0 12.6208 3.15402
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 8257 Ranked High confidence 13730.5 1.66289
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 0.355148 Squared Low confidence 3.41692 9.62112
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] 6909 Ranked 9830 1.42278
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 44 1 High confidence 58 1.31818
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 14.4058 0 Rooted Low confidence 7.90063 1.82337
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 773 Measured High confidence 148 5.22297

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/