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 2280 to 2329 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
570 swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077] Measured 4134.77 4691.24 1.13458
571 ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Rooted 62.7424 67.9648 1.08324
malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Ranked 238.529 254.099 1.06528
n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Squared 17799.8 21105.3 1.1857
swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078] Measured 4134.77 4691.24 1.13458
572 cbf1 interacting corepressor. [refseq;acc:nm_004882] Ranked 227.86 213.945 1.06504
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Rooted 62.7424 67.9648 1.08324
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] Squared 17799.8 21105.3 1.1857
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] Measured 4134.77 4691.24 1.13458
573 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Ranked 227.86 213.945 1.06504
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Measured 6739.43 7644.55 1.1343
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Rooted 62.7427 67.9648 1.08323
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Squared 17799.8 21105.3 1.1857
574 ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Rooted 62.7456 67.9646 1.08318
hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Squared 26570.7 31504.6 1.18569
homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Measured 6739.61 7644.58 1.13428
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Ranked 221.807 208.264 1.06503
575 dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4]
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Measured 6739.63 7644.59 1.13427
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Rooted 121.695 131.815 1.08316
vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] Squared 26570.7 31504.6 1.18569
576 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Ranked 235.18 250.419 1.0648
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Rooted 121.695 131.815 1.08316
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Measured 6739.7 7644.6 1.13426
577 acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] Squared 36109.8 42811.6 1.1856
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Ranked 224.606 210.944 1.06477
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Measured 6739.81 7644.62 1.13425
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Rooted 121.695 131.815 1.08316
578 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Measured 6739.81 7644.62 1.13425
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Rooted 121.695 131.815 1.08316
importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] Squared 23534.9 27890.2 1.18506
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Ranked 224.606 210.944 1.06477
579 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Measured 6739.82 7644.62 1.13425
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Rooted 121.695 131.815 1.08316
voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] Squared 23526.4 27879.4 1.18503
zinc finger protein t86. [swissprot;acc:o00488] Ranked 246.805 231.796 1.06475
580 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Measured 6739.83 7644.63 1.13425
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Rooted 121.695 131.815 1.08316
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Squared 23526.4 27879.3 1.18502
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Ranked 236.751 252.038 1.06457
581 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Measured 6739.82 7644.63 1.13425
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Rooted 121.695 131.815 1.08316
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Ranked 237.28 252.492 1.06411
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] Squared 23526.4 27879.3 1.18502
582 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Measured 6739.82 7644.62 1.13425
homeobox protein barh-like 1. [swissprot;acc:q9hbu1] Ranked 237.28 252.492 1.06411
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Rooted 121.695 131.815 1.08316
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557] Squared 23526.4 27879.3 1.18502
583 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154]

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/