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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1568 to 1617 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
196 t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] Measured 0 465.37 562.085 1.20782
197 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Squared 479.099 335.74 1.42699
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Measured 2145.97 1784.22 1.20275
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Ranked 1 263.215 231.407 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
importin 4. [refseq;acc:nm_024658] Ranked 0 12337.6 13788.9 1.11763
keratin associated protein 1.5. [refseq;acc:nm_031957] Rooted 23.8722 20.9331 1.1404
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 1 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
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Squared 0 1679.15 1177.18 1.42642
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Rooted 23.8722 20.9331 1.1404
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Squared 1 71062.2 95488.6 1.34373
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Ranked 0 11781.5 10545.3 1.11723
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Measured 247.333 206 1.20065
199 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Ranked 11781.8 10545.7 1.11721
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Measured 1230.54 1026.18 1.19915
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Rooted 23.8722 20.9331 1.1404
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] Squared 21.8736 31.1879 1.42582
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Ranked 1 242.735 276.059 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
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 0 578.056 482.7 1.19755
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Ranked 1 242.718 276.018 1.1372
gk001 protein. [refseq;acc:nm_020198] Squared 71062.2 95488.6 1.34373
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Rooted 0 23.8722 20.9333 1.14039
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 1 61.2893 70.3856 1.14842
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Ranked 0 8786.74 7870.3 1.11644
transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] Squared 5317.39 3738.08 1.42249
201 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 351.996 499.177 1.41813
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 1 71033.4 95440.2 1.3436
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] Rooted 61.2893 70.3856 1.14842
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 0 23.8722 20.9336 1.14038
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Ranked 16853 15123 1.1144
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 1 240.133 211.382 1.13601
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] Measured 0 6804.88 5690.63 1.1958
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 1 4810.22 6075.04 1.26294
202 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Squared 71030.1 95434.8 1.34358
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Measured 0 606.049 723.75 1.19421
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Squared 3339.18 2360.97 1.41433
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] Measured 1 4812.01 6076.09 1.26269
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Rooted 0 23.8722 20.9336 1.14038
serpin b11. [swissprot;acc:q96p15] Ranked 16853 15123 1.1144
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 1 201.478 228.784 1.13553
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Rooted 57.3527 65.7973 1.14724
203 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Measured 11757.8 9352.11 1.25723

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/