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 3180 to 3229 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
199 source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Rooted Divided 1 61.2893 70.3856 1.14842
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Squared Subtracted 0 799.337 432.882 366.455
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Divided 1 71062.2 95488.6 1.34373
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Rooted Subtracted 0 10.9527 8.13999 2.81271
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Measured 385 543 158
200 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Ranked 1 241.808 267.335 25.527
aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Measured 10635.3 12111.4 1476.1
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Divided 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
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Measured Subtracted 0 1705.19 1547.2 157.99
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Rooted Divided 23.8722 20.9333 1.14039
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Squared Subtracted 1 42411.6 55802.1 13390.5
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 0 129.158 488.851 359.693
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Rooted Divided 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
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Rooted Subtracted 1 63.5827 53.0856 10.4971
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] 0 11.5003 8.68906 2.81124
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Ranked 13483.3 14685.4 1202.1
transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] Squared Divided 5317.39 3738.08 1.42249
201 60s ribosomal protein l11. [swissprot;acc:p39026] Ranked Subtracted 1 241.828 267.346 25.518
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 0 6814 8009 1195
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Squared Divided 351.996 499.177 1.41813
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 1 71033.4 95440.2 1.3436
chromodomain y-like protein 2. [refseq;acc:nm_152342] Rooted Subtracted 0 33.0227 30.2263 2.7964
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] 1 138.375 127.926 10.449
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Squared 0 468.221 113.017 355.204
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 Divided 1 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
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Squared Subtracted 1 42411.6 55802.1 13390.5
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Measured 0 6699.82 6856.28 156.46
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Ranked Divided 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
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Subtracted 10603.5 12069.5 1466
202 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked 240.758 266.079 25.321
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Rooted 0 10.9038 8.12243 2.78137
arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] Measured 2039.07 2194.52 155.45
calsyntenin-1 precursor. [swissprot;acc:o94985] 1 10603.5 12069.5 1466
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Squared Divided 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
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Squared Subtracted 1 42411.6 55802.1 13390.5
serpin b11. [swissprot;acc:q96p15] Ranked Divided 0 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

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/