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 Value Type Network Comparison Type red Filtered Interaction Map network_comparison green
Results: HTML CSV LaTeX Showing element 51 to 100 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
description
red
Filtered
Interaction Map
network_comparison
green
13 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 288.754 1 High confidence 1.3585 212.554
sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] 7435.56 0 Low confidence 1.63963 12191.6
14 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 56.6768 1 High confidence 1.32952 75.3531
dystrophin. [swissprot;acc:p11532] 10232.5 0 1.76446 18054.8
ptd016 protein. [refseq;acc:nm_016125] 18050 Low confidence 1.60673 11234
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] 37.9984 1 1.30207 29.1831
15 adenomatous polyposis coli like. [refseq;acc:nm_005883] 12074.1 0 1.5892 7597.61
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 56.7244 1 High confidence 1.32914 75.3948
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 255.046 Low confidence 1.26035 202.362
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] 19403 0 High confidence 1.72211 11267
16 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 7395 Low confidence 1.57201 11625
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 12170.7 High confidence 1.69839 20670.6
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 56.7252 1 1.32913 75.3954
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 305.472 Low confidence 1.2355 247.246
17 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 56.7841 High confidence 1.32866 75.447
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 11543 0 1.69451 6812
gbp protein isoform a. [refseq;acc:nm_017870] 305.399 1 Low confidence 1.23537 247.213
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] 8082.33 0 1.53462 5266.67
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 185.678 1 High confidence 1.32082 245.247
early hematopoietic zinc finger. [refseq;acc:nm_015461] 5850.23 0 Low confidence 1.52187 8903.28
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 22286 High confidence 1.68629 13216
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] 305.303 1 Low confidence 1.2352 247.169
19 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 185.678 High confidence 1.32082 245.247
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 22286 0 1.68629 13216
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 3208.8 Low confidence 1.5182 4871.6
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] 304.548 1 1.23387 246.824
20 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 185.678 High confidence 1.32082 245.247
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] 22422 0 Low confidence 1.4984 14964
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 22286 High confidence 1.68629 13216
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] 304.359 1 Low confidence 1.23354 246.737
21 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 6313.38 0 High confidence 1.68236 10621.4
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 3859 Low confidence 1.49458 2582
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 185.678 1 High confidence 1.32082 245.247
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] 198 Low confidence 1.21472 163
22 cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] 11515 0 1.46371 7867
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 185.678 1 High confidence 1.32082 245.247
n33 protein. [swissprot;acc:q13454] 198 Low confidence 1.21472 163
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 20989 0 High confidence 1.68195 12479
23 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 58 1 1.31818 44
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 15520.4 0 1.67148 9285.44
implantation-associated protein. [refseq;acc:nm_032121] 198 1 Low confidence 1.21472 163
serpin b12. [swissprot;acc:q96p63] 14604.2 0 1.44743 21138.6
24 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 13730.5 High confidence 1.66289 8257
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] 188.298 1 Low confidence 1.21355 228.509
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 14592 0 1.44694 21113.7
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 58 1 High confidence 1.31818 44
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] 286.396 Low confidence 1.20094 238.476
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 13730.5 0 High confidence 1.66289 8257
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] 9830 Low confidence 1.42278 6909
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 58 1 High confidence 1.31818 44

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/