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.


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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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2277 to 2326 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
570 no value Rooted disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 62.7424 67.9648 1.08324
MRE11A Squared double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] 52623.3 44380.3 1.18574
SFRS11 Ranked splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] 229.709 215.631 1.06529
SMARCD2 Measured 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] 4134.77 4691.24 1.13458
571 FTL Rooted ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] 62.7424 67.9648 1.08324
GALK2 Squared n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] 17799.8 21105.3 1.1857
MDH2 Ranked malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] 238.529 254.099 1.06528
SMARCD3 Measured 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] 4134.77 4691.24 1.13458
572 no value Ranked cbf1 interacting corepressor. [refseq;acc:nm_004882] 227.86 213.945 1.06504
Squared galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] 17799.8 21105.3 1.1857
DLGAP4 Rooted disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] 62.7424 67.9648 1.08324
SMARCD1 Measured 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] 4134.77 4691.24 1.13458
573 FTMT Rooted mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] 62.7427 67.9648 1.08323
GALE Squared udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] 17799.8 21105.3 1.1857
GPATCH1 Ranked evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] 227.86 213.945 1.06504
HOXA10 Measured homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] 6739.43 7644.55 1.1343
574 ASNSD1 Squared hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] 26570.7 31504.6 1.18569
FTHL17 Rooted ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 62.7456 67.9646 1.08318
HOXB9 Measured homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 6739.61 7644.58 1.13428
MOBKL3 Ranked preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] 221.807 208.264 1.06503
575 no value Rooted homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 121.695 131.815 1.08316
ATP6V1A Squared 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] 26570.7 31504.6 1.18569
DNAJB11 Ranked 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] 221.807 208.264 1.06503
HOXA9 Measured homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] 6739.63 7644.59 1.13427
576 no value Ranked dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 235.18 250.419 1.0648
ASNS Squared asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] 26570.7 31504.6 1.18569
HOXB4 Rooted homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 121.695 131.815 1.08316
HOXC9 Measured homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 6739.7 7644.6 1.13426
577 ASAH1 Squared acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] 36109.8 42811.6 1.1856
GABRG3 Measured gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 6739.81 7644.62 1.13425
HOXC5 Rooted homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 121.695 131.815 1.08316
PRSS7 Ranked enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 224.606 210.944 1.06477
578 no value Rooted homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 121.695 131.815 1.08316
FOXG1 Measured forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 6739.81 7644.62 1.13425
KPNA6 Squared importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] 23534.9 27890.2 1.18506
SF3B2 Ranked splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 224.606 210.944 1.06477
579 GABRG1 Measured gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 6739.82 7644.62 1.13425
HOXD4 Rooted homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 121.695 131.815 1.08316
KCNAB3 Squared voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] 23526.4 27879.4 1.18503
ZNF593 Ranked zinc finger protein t86. [swissprot;acc:o00488] 246.805 231.796 1.06475
580 GABRA2 Measured gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 6739.83 7644.63 1.13425
HOXB5 Rooted homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 121.695 131.815 1.08316
YIF1A Squared yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] 23526.4 27879.3 1.18502
ZNRD1 Ranked zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] 236.751 252.038 1.06457
581 GABRA6 Measured gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 6739.82 7644.63 1.13425
HOXA5 Rooted homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 121.695 131.815 1.08316
KCNAB1 Squared voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] 23526.4 27879.3 1.18502
TLX3 Ranked t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] 237.28 252.492 1.06411
582 no value Rooted homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 121.695 131.815 1.08316
BARX1 Ranked homeobox protein barh-like 1. [swissprot;acc:q9hbu1] 237.28 252.492 1.06411

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/