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

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/