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.


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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 1730 to 1779 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
109 aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] Squared Subtracted 0 5219.15 3979.89 1239.26
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 1 88432.6 58423.3 30009.3
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Measured Divided 0 100 144 1.44
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Ranked 14466.8 12031.7 1.20239
glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Subtracted 1 209.299 249.187 39.888
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Divided 266.933 333.281 1.24856
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Squared 19321 12542.6 1.54043
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Rooted Subtracted 30.8986 46.4619 15.5633
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Ranked 0 9940.69 11929 1988.31
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] Rooted Divided 2.64575 3.38392 1.279
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Measured 1 4366.44 5899.76 1.35116
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Rooted Subtracted 0 21.0524 16.4963 4.5561
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Measured 934.726 1222.89 288.164
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Rooted Divided 1 49.2923 62.3969 1.26585
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Squared 0 16.4056 33.4891 2.04132
110 deltex 2. [refseq;acc:nm_020892] Ranked 1 333.144 267.393 1.2459
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Measured Subtracted 0 528.5 816.5 288
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Ranked Divided 12584.5 10470.6 1.20189
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Rooted Subtracted 54.8943 59.4407 4.5464
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Ranked 1 209.299 249.187 39.888
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] 0 14864.7 16820.7 1956
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Rooted 1 33.9632 18.4255 15.5377
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Squared Divided 19321 12542.6 1.54043
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Measured Subtracted 17385.9 14889.2 2496.7
pnas-18. [sptrembl;acc:q9bzu3] Squared 87787.3 58155.8 29631.5
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Measured Divided 4366.44 5899.76 1.35116
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Rooted 0 7.7419 6.06104 1.27732
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] Measured 1833 2637 1.43863
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] Squared Subtracted 5219.15 3979.89 1239.26
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Rooted Divided 1 49.293 62.3973 1.26585
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] Squared 0 16.4056 33.4891 2.04132
111 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Subtracted 1 79779.8 108084 28304.2
collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Rooted 0 35.0775 30.5361 4.5414
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Ranked Divided 1 332.925 267.274 1.24563
glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Subtracted 209.299 249.187 39.888
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Rooted 33.9632 18.4255 15.5377
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Squared Divided 19321 12542.6 1.54043
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Measured 4366.44 5899.76 1.35116
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Ranked 0 9940.69 11929 1.20002
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] Subtracted 13255.4 15183.2 1927.8
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Measured Divided 2965.5 2063 1.43747
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Squared Subtracted 3088.94 4269.96 1181.02
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Rooted Divided 21.0524 16.4963 1.27619
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Measured Subtracted 10247.8 10535 287.2
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 1 12365.2 14824.9 2459.7
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Rooted Divided 49.2923 62.3969 1.26585
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] Squared 0 16.4056 33.4891 2.04132
112 40s ribosomal protein s26. [swissprot;acc:p02383] Ranked 14269.7 17098 1.1982
autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Measured Subtracted 1 11757.8 9352.11 2405.69
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] Rooted Divided 0 22.4608 17.665 1.27149

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/