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 2282 to 2331 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
571 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
Rooted homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 121.695 131.815 1.08316
578 Measured forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 6739.81 7644.62 1.13425
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
Squared importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] 23534.9 27890.2 1.18506
Rooted homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 121.695 131.815 1.08316
579 Measured gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 6739.82 7644.62 1.13425
Ranked zinc finger protein t86. [swissprot;acc:o00488] 246.805 231.796 1.06475
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
Rooted homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 121.695 131.815 1.08316
580 Measured gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 6739.83 7644.63 1.13425
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
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
Rooted homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 121.695 131.815 1.08316
581 Measured gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 6739.82 7644.63 1.13425
Ranked t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] 237.28 252.492 1.06411
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
Rooted homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 121.695 131.815 1.08316
582 Measured gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 6739.82 7644.62 1.13425
Ranked homeobox protein barh-like 1. [swissprot;acc:q9hbu1] 237.28 252.492 1.06411
Squared similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557] 23526.4 27879.3 1.18502
Rooted homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 121.695 131.815 1.08316
583 Measured interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 6739.81 7644.62 1.13425
Ranked opsin 4 (melanopsin). [swissprot;acc:q9uhm6] 237.28 252.492 1.06411
Squared aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] 23526.4 27879.3 1.18502

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/