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 [...,...].
Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
Hugo
description
Filtered
red
green
network_comparison
1 ARFGAP3 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 0 4294 15915 3.70633
UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 1 10 24 2.4
2 no value mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 15 28 1.86667
STARD3 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 0 5865 14977 2.55362
3 no value nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 4475.84 11083.9 2.47638
PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 1 15 28 1.86667
4 no value mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 8906 21883 2.45711
PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1 15 28 1.86667
5 no value ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 0 5510.5 11965.7 2.17144
PSCD4 cytohesin 4. [swissprot;acc:q9uia0] 1 15 28 1.86667
6 PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]
UBE3B ubiquitin protein ligase. [refseq;acc:nm_130466] 0 7523 15339.2 2.03897
7 HLX homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 215 322 1.49767
PERLD1 cab2. [refseq;acc:nm_033419] 0 21866 10950 1.99689
8 no value nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 11525 21888 1.89918
HBS1L hbs1-like. [refseq;acc:nm_006620] 1 215 322 1.49767
9 TBL1Y transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 0 11525 21888 1.89918
XAB1 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1 212 309 1.45755
10 ATPBD1C protein x 0004. [refseq;acc:nm_016301]
FBP2 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 0 7509.39 14178.1 1.88805
11 ATP9A potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 11627 6248 1.86092
RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] 1 337 232 1.45259
12 FPGS folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 0 9429.18 5208.84 1.81023
RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 337 232 1.45259
13 no value heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 0 5210.5 9264.5 1.77804
UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1 288.754 212.554 1.3585
14 no value dystrophin. [swissprot;acc:p11532] 0 10232.5 18054.8 1.76446
ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 1 56.6768 75.3531 1.32952
15 no value 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] 0 19403 11267 1.72211
MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 1 56.7244 75.3948 1.32914
16 CCNH cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 0 12170.7 20670.6 1.69839
MAP1LC3A 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
17 no value 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
ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 1 56.7841 75.447 1.32866
18 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 22286 13216 1.68629
GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 1 185.678 245.247 1.32082
19 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 22286 13216 1.68629
PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 1 185.678 245.247 1.32082
20 no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 22286 13216 1.68629
PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1 185.678 245.247 1.32082
21 ACRC acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 0 6313.38 10621.4 1.68236
MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 1 185.678 245.247 1.32082
22 PNPO pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0 20989 12479 1.68195
PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 1 185.678 245.247 1.32082
23 HGS 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
MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 1 58 44 1.31818
24 no value ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 13730.5 8257 1.66289
PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 1 58 44 1.31818
25 no value lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 13730.5 8257 1.66289
PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 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
- Hugo is the HGNC identifier if it exists
- 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/