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.


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Rank Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4558 to 4607 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
red
green
network_comparison
570 SMARCD2 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] Divided Measured 4134.77 4691.24 1.13458
SNX17 sorting nexin 17. [swissprot;acc:q15036] Subtracted Ranked 228.639 242.258 13.619
ZNF593 zinc finger protein t86. [swissprot;acc:o00488] Rooted 51.0466 56.024 4.9774
571 FTL ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Divided 62.7424 67.9648 1.08324
FTMT mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Subtracted Squared 31994.3 36720 4725.7
GALK2 n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Divided 17799.8 21105.3 1.1857
MDH2 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Ranked 238.529 254.099 1.06528
MOBKL3 preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Subtracted 221.807 208.264 13.543
OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Measured 3856.29 4624.15 767.86
SMARCD3 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] Divided 4134.77 4691.24 1.13458
SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] Subtracted Rooted 50.519 45.5497 4.9693
572 no value cbf1 interacting corepressor. [refseq;acc:nm_004882] Divided Ranked 227.86 213.945 1.06504
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
CREG2 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Subtracted 31994 36719.6 4725.6
DLGAP4 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Divided Rooted 62.7424 67.9648 1.08324
DNAJB11 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] Subtracted Ranked 221.807 208.264 13.543
PCYT1A cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Rooted 50.3803 45.4193 4.961
PYCR2 pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Measured 5277.4 6042.88 765.48
SMARCD1 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] Divided 4134.77 4691.24 1.13458
573 no value dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Subtracted Squared 31994 36719.6 4725.6
FLAD1 fad synthetase. [refseq;acc:nm_025207] Rooted 50.3803 45.4193 4.961
FTMT mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Divided 62.7427 67.9648 1.08323
GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Squared 17799.8 21105.3 1.1857
GNL2 autoantigen ngp-1. [swissprot;acc:q13823] Subtracted Ranked 250.302 236.817 13.485
GPATCH1 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Divided 227.86 213.945 1.06504
HOXA10 homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Measured 6739.43 7644.55 1.1343
PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Subtracted 5281.11 6044.61 763.5
574 no value bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Rooted 50.3803 45.4193 4.961
ASNSD1 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Divided Squared 26570.7 31504.6 1.18569
DLGAP1 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Subtracted 31994 36719.6 4725.6
FTHL17 ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Divided Rooted 62.7456 67.9646 1.08318
HOXB9 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Measured 6739.61 7644.58 1.13428
LGALS4 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Subtracted 7817.9 8575.12 757.22
MOBKL3 preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Divided Ranked 221.807 208.264 1.06503
POLR2D dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] Subtracted 237.554 250.823 13.269
575 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided Rooted 121.695 131.815 1.08316
AHCYL1 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Subtracted Squared 31994 36719.6 4725.6
ATP6V1A 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] Divided 26570.7 31504.6 1.18569
CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Subtracted Ranked 223.282 210.136 13.146
DNAJB11 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] Divided 221.807 208.264 1.06503
HOXA9 homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Measured 6739.63 7644.59 1.13427
LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Subtracted Rooted 50.3803 45.4193 4.961
SPTBN5 spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Measured 7813.48 8570.11 756.63
576 no value dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Divided Ranked 235.18 250.419 1.0648
ASNS asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] Squared 26570.7 31504.6 1.18569
HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Rooted 121.695 131.815 1.08316
HOXC9 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Measured 6739.7 7644.6 1.13426
KIAA0430 limkain b1. [refseq;acc:nm_019081] Subtracted Squared 31994 36719.6 4725.6
PAPSS1 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Rooted 50.3803 45.4193 4.961
POLR2G dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Ranked 232.469 245.613 13.144

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/