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.


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 description Gene Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6762 to 6811 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
Hugo
Value Type
red
green
network_comparison
846 keratin associated protein 4.4. [refseq;acc:nm_032524] Divided KRTAP4-4 Squared 31100.2 36086.5 1.16033
methyltransferase like 2. [refseq;acc:nm_018396] no value Ranked 147.211 153.371 1.04184
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Subtracted Measured 5797.88 6391.75 593.87
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] MTO1 Squared 25580.6 29466.1 3885.5
parafibromin. [refseq;acc:nm_024529] CDC73 Ranked 239.704 230.991 8.713
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Divided PRKCZ Rooted 65.0565 69.1533 1.06297
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Subtracted SPRY2 59.6869 63.6262 3.9393
847 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Divided no value Squared 31100.1 36086.4 1.16033
beta-catenin (pro2286). [swissprot;acc:p35222] Subtracted CTNNB1 Rooted 60.2378 64.1631 3.9253
cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Divided DYNLT1 Ranked 147.211 153.371 1.04184
cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] NCK2 Measured 6776.85 7485.55 1.10458
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Subtracted MYCL1 Ranked 227.604 219.001 8.603
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] PRSS12 Squared 24242.8 28127.6 3884.8
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] NUP88 Measured 5797.88 6391.75 593.87
wd-repeat protein bing4. [swissprot;acc:o15213] Divided WDR46 Rooted 51.7527 55.0117 1.06297
848 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] FZR1 Ranked 147.211 153.371 1.04184
phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] Subtracted CDS1 Measured 6441.56 7034.86 593.3
pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] Divided LIMS1 Squared 31100.1 36086.4 1.16033
protein bap28. [swissprot;acc:q9h583] HEATR1 Rooted 51.1817 54.4034 1.06295
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Subtracted no value 51.0687 47.1439 3.9248
ring finger protein 44. [refseq;acc:nm_014901] RNF44 Squared 24242.8 28127.6 3884.8
wd-repeat protein bing4. [swissprot;acc:o15213] Divided WDR46 Measured 4066.56 4491.65 1.10453
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Subtracted WIPF1 Ranked 206.214 197.614 8.6
849 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] HTATIP Rooted 61.3164 65.2371 3.9207
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] Divided DDB1 Measured 6194.15 6839.37 1.10417
integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] ILK Squared 31100.1 36086.4 1.16033
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] Subtracted PIK3R1 24242.8 28127.6 3884.8
proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Divided PCSK5 Ranked 147.211 153.371 1.04184
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] RRS1 Rooted 124.41 117.043 1.06294
solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] Subtracted SLC13A4 Measured 6439.63 7032.19 592.56
transcription factor iib. [refseq;acc:nm_013242] C16orf80 Ranked 206.068 197.471 8.597
850 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Divided CPSF4 107.842 112.329 1.04161
hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Subtracted ASNSD1 Rooted 62.7551 66.6474 3.8923
propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Divided PCCB Measured 6194.15 6839.37 1.10417
ring finger protein 38. [refseq;acc:nm_022781] Subtracted RNF38 Squared 24242.8 28127.6 3884.8
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Divided PPP1CA Rooted 124.41 117.043 1.06294
solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] Subtracted SLC13A3 Measured 6439.66 7032.22 592.56
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] SFRS8 Ranked 206.068 197.471 8.597
star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4] Divided STARD4 Squared 31100.1 36086.4 1.16033
851 casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] CSNK2A1P Measured 4307.12 4755.03 1.10399
n-myc proto-oncogene protein. [swissprot;acc:p04198] Subtracted MYCN Ranked 227.601 219.008 8.593
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] PIK3R3 Squared 24242.8 28127.6 3884.8
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Divided ATP2C2 Rooted 65.1512 69.252 1.06294
ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] RSU1 Squared 31100.1 36086.4 1.16033
solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] Subtracted SLC13A1 Measured 6439.63 7032.19 592.56
trs85 homolog. [swissprot;acc:q9y2l5] Divided KIAA1012 Ranked 107.842 112.329 1.04161
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] Subtracted ATP6V1A Rooted 62.7551 66.6474 3.8923
852 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] ASNS
casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Divided CSNK2A2 Measured 4307.12 4755.03 1.10399
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Subtracted GABPA Ranked 227.596 219.017 8.579

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/