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.


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 Gene Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 758 to 807 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
190 DDOST Measured dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 4571.89 5864.86 1.28281
GABARAP Rooted gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 149.165 129.699 1.15009
SNRP70 Ranked u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 226.582 198.444 1.14179
191 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
AQP5 Squared aquaporin 5. [swissprot;acc:p55064] 71388.5 96035.2 1.34525
PLDN Rooted pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 63.1192 72.584 1.14995
SF3B1 Measured splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 4638.1 5923.4 1.27712
192 AQP2 Squared aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] 71387.4 96033.4 1.34524
ARAF Measured a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 17757.5 14008 1.26767
MSI2 Ranked musashi 2 isoform a. [refseq;acc:nm_138962] 227.491 199.458 1.14055
SF4 Rooted splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 53.6107 61.5862 1.14877
193 MIP Squared lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] 71386.9 96032.5 1.34524
MSI1 Ranked musashi 1. [refseq;acc:nm_002442] 227.491 199.458 1.14055
NOSTRIN Rooted nostrin. [refseq;acc:nm_052946] 59.6399 51.9242 1.1486
RAF1 Measured raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] 17756.5 14007.3 1.26766
194 AQP1 Squared aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] 71346.6 95965.1 1.34505
CCNG2 Measured cyclin g2. [swissprot;acc:q16589] 17738.6 13995.7 1.26743
SNF8 Rooted eap30 subunit of ell complex. [refseq;acc:nm_007241] 59.6399 51.9242 1.1486
ZC3H14 Ranked nuclear protein ukp68. [refseq;acc:nm_024824] 227.491 199.458 1.14055
195 CCNG1 Measured cyclin g1 (cyclin g). [swissprot;acc:p51959] 17738.5 13995.6 1.26743
PRPF40B Ranked huntingtin interacting protein c. [refseq;acc:nm_012272] 227.971 200.417 1.13748
SLC39A6 Rooted liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 59.6399 51.9242 1.1486
SSR4 Squared translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] 71062.4 95488.9 1.34373
196 CLSTN1 calsyntenin-1 precursor. [swissprot;acc:o94985]
FOXP4 Ranked forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 263.215 231.407 1.13745
GAD2 Rooted glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] 59.6399 51.9242 1.1486
PPP2R5E Measured serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] 17738.5 13995.7 1.26742
197 no value Squared succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] 71062.4 95488.9 1.34373
FOXP1 Ranked forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 263.215 231.407 1.13745
NAPG Rooted gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 59.6399 51.9242 1.1486
PPP2R5A Measured serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] 17738.5 13995.7 1.26742
198 BRAF b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 17710.9 13977.7 1.26708
FOXP3 Ranked forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 263.191 231.394 1.13741
GAD1 Rooted glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 59.6399 51.9242 1.1486
PTPRB Squared protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] 71062.2 95488.6 1.34373
199 EGFL8 Ranked palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 242.735 276.059 1.13729
PPP2CA Measured serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 4916.8 3888.18 1.26455
PRSS16 Squared thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] 71062.2 95488.6 1.34373
STT3B Rooted source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 61.2893 70.3856 1.14842
200 BCAR1 Measured crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 4808.79 6074.21 1.26315
CCDC47 Squared gk001 protein. [refseq;acc:nm_020198] 71062.2 95488.6 1.34373
EGFL7 Ranked egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 242.718 276.018 1.1372
STT3A Rooted oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 61.2893 70.3856 1.14842
201 CCT4 Measured t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 4810.22 6075.04 1.26294
CLSTN2 Squared calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 71033.4 95440.2 1.3436
DDOST Rooted dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 61.2893 70.3856 1.14842
SF4 Ranked splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 240.133 211.382 1.13601
202 no value Rooted splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 57.3527 65.7973 1.14724
CLSTN3 Squared calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 71030.1 95434.8 1.34358
NEDD9 Measured enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 4812.01 6076.09 1.26269

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/