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 1768 to 1817 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
111 protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Ranked Divided 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
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Squared Subtracted 1 96730.5 69286.7 27443.8
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Ranked 275.754 235.908 39.846
guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] Rooted 0 31.1565 35.6653 4.5088
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Ranked 8335.82 10228.3 1892.48
lats homolog 1. [refseq;acc:nm_004690] Measured Divided 160 112.25 1.42539
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Squared 138.269 68.9705 2.00476
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 1 19321 12542.6 1.54043
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Subtracted 0 12235.5 13399.2 1163.7
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Measured 1095.42 812.166 283.254
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] Rooted 1 33.9632 18.4255 15.5377
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Ranked Divided 332.874 267.246 1.24557
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Measured 4366.44 5899.76 1.35116
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Rooted 49.3267 62.4167 1.26537
113 60s ribosomal protein l7. [swissprot;acc:p18124] Squared Subtracted 0 5826.27 6955.21 1128.94
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Rooted Divided 1 80.4705 101.526 1.26165
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Squared Subtracted 96602.7 69211.2 27391.5
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Measured 4800.81 7132.71 2331.9
db83 protein. [swissprot;acc:p57088] Rooted 33.9632 18.4255 15.5377
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Measured Divided 4366.44 5899.76 1.35116
fos-related antigen 2. [swissprot;acc:p15408] Rooted Subtracted 0 44.3292 39.9005 4.4287
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Squared Divided 387.336 770.962 1.99042
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Ranked 1 332.874 267.246 1.24557
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Subtracted 0 8335.82 10228.3 1892.48
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Squared Divided 1 19321 12542.6 1.54043
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Rooted 0 72.1137 56.7758 1.27015
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Ranked 5673.33 6797.56 1.19816
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Subtracted 1 194.372 234.204 39.832
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Measured Divided 0 160 112.25 1.42539
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Subtracted 3117.17 2833.94 283.23
114 60s ribosomal protein l37a. [swissprot;acc:p12751] 305.45 26.1599 279.29
autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Squared 1 67438.6 40697 26741.6
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Ranked 229.818 267.265 37.447
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Rooted Divided 80.4705 101.526 1.26165
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Ranked 0 8871.11 10603.2 1.19525
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Squared Subtracted 5868.74 4797.35 1071.39
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Measured 1 13768.2 11466 2302.2
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Divided 0 671.769 472.945 1.4204
guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Rooted Subtracted 1 40.225 24.7051 15.5199

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/