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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4008 to 4057 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
251 histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Squared Subtracted 1 34506.3 43476 8969.7
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Ranked 0 12463.5 11482.6 980.9
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Divided 10551.6 11573.6 1.09686
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Measured 1225.08 1079.38 1.13498
max protein. [swissprot;acc:p25912] Rooted 1 56.3054 63.7148 1.13159
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Ranked 186.172 166.661 1.11707
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Measured 6417.18 7859.6 1.22477
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Squared 0 25574.2 20063.8 1.27464
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Rooted Subtracted 17.1346 14.7899 2.3447
252 centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Squared 1 51286.6 42334.5 8952.1
crk-like protein. [swissprot;acc:p46109] Measured Divided 6417.18 7859.6 1.22477
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Subtracted 0 2039.47 2164.92 125.45
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Ranked Divided 1 237.292 212.457 1.11689
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Measured Subtracted 9648.27 10994.9 1346.63
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Ranked Divided 0 10551.6 11573.5 1.09685
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] Rooted 21.1331 19.1063 1.10608
mad protein (max dimerizer). [swissprot;acc:q05195] Ranked Subtracted 1 228 204.333 23.667
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Rooted Divided 51.6736 58.4422 1.13099
pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Squared 69165 52991.7 1.3052
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Subtracted 0 366.272 222.124 144.148
sedlin. [swissprot;acc:o14582] Rooted 1 116.061 125.434 9.373
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Squared Divided 0 803.941 631.169 1.27373
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Measured 1225.08 1079.38 1.13498
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Ranked Subtracted 12748.1 11770.9 977.2
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Rooted 17.1395 14.7969 2.3426
253 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Ranked 9586.97 10560 973.03
b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Squared Divided 1 69165 52991.7 1.3052
cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] Subtracted 0 399.199 542.77 143.571
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Measured 1 9642.22 10986.4 1344.18
espin. [refseq;acc:nm_031475] Divided 0 1225.07 1079.38 1.13498
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Squared Subtracted 1 39478.8 48419 8940.2
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Measured 0 556 681 125
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Ranked Divided 10551.6 11573.5 1.09685
mad protein (max dimerizer). [swissprot;acc:q05195] 1 228 204.333 1.11583
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Squared 0 46977 36903.3 1.27298
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Ranked Subtracted 1 251.679 228.037 23.642
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Measured Divided 6417.18 7859.59 1.22477
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Rooted 0 8.05424 8.90701 1.10588
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Subtracted 22.3157 24.6207 2.305
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 1 53.5956 60.465 1.12817
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Subtracted 116.061 125.434 9.373
254 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Measured Divided 0 1318.22 1495.66 1.13461
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Rooted Subtracted 22.315 24.6198 2.3048
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] Squared Divided 220.878 173.801 1.27087
bet3 homolog. [swissprot;acc:o43617] Rooted Subtracted 1 116.061 125.434 9.373
dc11 protein. [refseq;acc:nm_020186] Measured 0 556 681 125
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] 1 9634.98 10976.2 1341.22
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Ranked Divided 0 10551.6 11573.5 1.09685
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Subtracted 1 227.999 204.357 23.642
neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Squared 0 399.199 542.77 143.571

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/