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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2258 to 2307 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
565 Ranked sedlin. [swissprot;acc:o14582] 129.219 121.261 1.06563
Squared fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 25287.7 30003.7 1.18649
Rooted limkain b1. [refseq;acc:nm_019081] 62.7424 67.9648 1.08324
566 Measured autoantigen ngp-1. [swissprot;acc:q13823] 3766.14 4274.79 1.13506
Ranked synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 129.219 121.261 1.06563
Squared transcription factor btf3 homolog 3. [swissprot;acc:q13892] 34268.1 40650.4 1.18625
Rooted putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] 62.7424 67.9648 1.08324
567 Measured deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] 10264.9 9043.51 1.13506
Ranked bet3 homolog. [swissprot;acc:o43617] 129.219 121.261 1.06563
Squared transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 34219.8 40585.4 1.18602
Rooted cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 62.7424 67.9648 1.08324
568 Measured grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] 4134.77 4691.24 1.13458
Ranked putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] 226.3 212.38 1.06554
Squared max protein. [swissprot;acc:p25912] 18764.5 22255 1.18602
Rooted disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] 62.7424 67.9648 1.08324
569 Measured grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] 4134.77 4691.24 1.13458
Ranked t54 protein. [swissprot;acc:q92917] 226.3 212.38 1.06554
Squared t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] 52623.3 44380.3 1.18574
Rooted kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] 62.7424 67.9648 1.08324
570 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
Ranked splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] 229.709 215.631 1.06529
Squared double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] 52623.3 44380.3 1.18574
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
571 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
Ranked malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] 238.529 254.099 1.06528
Squared n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] 17799.8 21105.3 1.1857
Rooted ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] 62.7424 67.9648 1.08324
572 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
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
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
573 Measured homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] 6739.43 7644.55 1.1343
Ranked evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] 227.86 213.945 1.06504
Squared udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] 17799.8 21105.3 1.1857
Rooted mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] 62.7427 67.9648 1.08323
574 Measured homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 6739.61 7644.58 1.13428
Ranked preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] 221.807 208.264 1.06503
Squared hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] 26570.7 31504.6 1.18569
Rooted ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 62.7456 67.9646 1.08318
575 Measured homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] 6739.63 7644.59 1.13427
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
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
Rooted homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 121.695 131.815 1.08316
576 Measured homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 6739.7 7644.6 1.13426
Ranked dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 235.18 250.419 1.0648
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
Rooted homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 121.695 131.815 1.08316
577 Measured gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 6739.81 7644.62 1.13425
Ranked enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 224.606 210.944 1.06477
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

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/