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.


Navigation/Query Panel:
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 6162 to 6211 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1541 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] Measured 5989.3 6427.17 1.07311
mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [swissprot;acc:p28482] Rooted 63.3022 65.6127 1.0365
myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Ranked 222.672 218.92 1.01714
1542 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Squared 2557.92 2299.4 1.11243
inositol polyphosphate multikinase. [refseq;acc:nm_152230] Measured 5466 5865.33 1.07306
symplekin. [swissprot;acc:q92797] Rooted 99.9862 96.4662 1.03649
trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Ranked 213.546 209.965 1.01706
1543 afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] Measured 5466 5865.33 1.07306
gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616] Ranked 213.546 209.965 1.01706
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Squared 2558.19 2299.7 1.1124
proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] Rooted 64.2792 66.6225 1.03646
1544 alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5] Measured 5466 5865.33 1.07306
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Squared 18161.1 20200 1.11227
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Ranked 219.762 216.081 1.01704
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Rooted 76.2612 79.0401 1.03644
1545 aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] Measured 5945.96 6380.28 1.07304
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Squared 18159.2 20197.6 1.11225
orphan nuclear receptor tr2. [swissprot;acc:p13056] Ranked 219.76 216.083 1.01702
zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] Rooted 76.2612 79.0401 1.03644
1546 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] Measured 5819.39 6244.37 1.07303
argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] Ranked 217.769 221.474 1.01701
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Squared 2559.56 2301.28 1.11223
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Rooted 76.2612 79.0401 1.03644
1547 cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] Measured 5397.21 5790.45 1.07286
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Squared 2560.11 2301.92 1.11216
myb-related protein b (b-myb). [swissprot;acc:p10244] Ranked 222.541 218.823 1.01699
proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] Rooted 64.2763 66.618 1.03643
1548 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] Squared 26408.9 29370.7 1.11215
60s ribosomal protein l28. [swissprot;acc:p46779] Measured 5987.29 6423.52 1.07286
myb-related protein a (a-myb). [swissprot;acc:p10243] Ranked 222.512 218.802 1.01696
r3h domain protein 1. [swissprot;acc:q15032] Rooted 62.1391 64.4016 1.03641
1549 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] 64.0988 66.426 1.03631
dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] Ranked 225.159 221.424 1.01687
glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] Measured 6025.86 6464.16 1.07274
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Squared 2560.39 2302.24 1.11213
1550 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Ranked 225.159 221.424 1.01687
dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] Measured 6025.86 6464.16 1.07274
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Squared 2561.25 2303.22 1.11203
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] Rooted 63.8741 66.193 1.0363
1551 adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] Ranked 225.159 221.424 1.01687
cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] Measured 5732.83 6149.86 1.07274
elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Squared 27018.7 30041.5 1.11188
phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2] Rooted 63.8741 66.1929 1.0363
1552 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] Ranked 225.159 221.424 1.01687
atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Measured 6025.86 6464.16 1.07274
phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] Rooted 63.8754 66.1935 1.03629
zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] Squared 27018.7 30041.5 1.11188
1553 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Ranked 215.389 211.833 1.01679
alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Rooted 54.3745 52.4728 1.03624
elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639] Squared 27018.7 30041.5 1.11188

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/