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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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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 751 to 800 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
188 source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Measured 4571.89 5864.86 1.28281
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Rooted 46.0352 53.0192 1.15171
189 mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Squared 41502.9 30836.8 1.34589
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Measured 4571.89 5864.86 1.28281
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Ranked 226.582 198.444 1.14179
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Rooted 46.0352 53.0192 1.15171
190 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Squared 71389.9 96037.6 1.34525
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] Measured 4571.89 5864.86 1.28281
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Rooted 149.165 129.699 1.15009
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Ranked 226.582 198.444 1.14179
191 aquaporin 5. [swissprot;acc:p55064] Squared 71388.5 96035.2 1.34525
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Ranked 226.582 198.444 1.14179
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Rooted 63.1192 72.584 1.14995
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Measured 4638.1 5923.4 1.27712
192 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
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] Squared 71387.4 96033.4 1.34524
musashi 2 isoform a. [refseq;acc:nm_138962] Ranked 227.491 199.458 1.14055
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Rooted 53.6107 61.5862 1.14877
193 lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Squared 71386.9 96032.5 1.34524
musashi 1. [refseq;acc:nm_002442] Ranked 227.491 199.458 1.14055
nostrin. [refseq;acc:nm_052946] Rooted 59.6399 51.9242 1.1486
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Measured 17756.5 14007.3 1.26766
194 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Squared 71346.6 95965.1 1.34505
cyclin g2. [swissprot;acc:q16589] Measured 17738.6 13995.7 1.26743
eap30 subunit of ell complex. [refseq;acc:nm_007241] Rooted 59.6399 51.9242 1.1486
nuclear protein ukp68. [refseq;acc:nm_024824] Ranked 227.491 199.458 1.14055
195 cyclin g1 (cyclin g). [swissprot;acc:p51959] Measured 17738.5 13995.6 1.26743
huntingtin interacting protein c. [refseq;acc:nm_012272] Ranked 227.971 200.417 1.13748
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Rooted 59.6399 51.9242 1.1486
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Squared 71062.4 95488.9 1.34373
196 calsyntenin-1 precursor. [swissprot;acc:o94985]
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Ranked 263.215 231.407 1.13745
glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Rooted 59.6399 51.9242 1.1486
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] Measured 17738.5 13995.7 1.26742
197 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Ranked 263.215 231.407 1.13745
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Rooted 59.6399 51.9242 1.1486
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] Measured 17738.5 13995.7 1.26742
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] Squared 71062.4 95488.9 1.34373
198 b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Measured 17710.9 13977.7 1.26708
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Ranked 263.191 231.394 1.13741
glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Rooted 59.6399 51.9242 1.1486
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Squared 71062.2 95488.6 1.34373
199 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Ranked 242.735 276.059 1.13729
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Measured 4916.8 3888.18 1.26455
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Rooted 61.2893 70.3856 1.14842
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Squared 71062.2 95488.6 1.34373
200 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Measured 4808.79 6074.21 1.26315
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Ranked 242.718 276.018 1.1372
gk001 protein. [refseq;acc:nm_020198] Squared 71062.2 95488.6 1.34373
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Rooted 61.2893 70.3856 1.14842

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/