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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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 6536 to 6585 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1634 pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Measured 9899.73 9251.16 1.07011
1635 5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] Squared 27290.4 30221.1 1.10739
b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Measured 9899.73 9251.16 1.07011
fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Rooted 61.2707 63.3571 1.03405
itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] Ranked 215.772 212.596 1.01494
1636 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Squared 28554.8 31619.6 1.10733
beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] Ranked 202.358 199.408 1.01479
wd-repeat protein 4. [swissprot;acc:p57081] Rooted 61.2707 63.3571 1.03405
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Measured 9899.73 9251.16 1.07011
1637 26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210] Ranked 202.358 199.408 1.01479
hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] Squared 12067.6 13362.6 1.10731
myelin p2 protein. [swissprot;acc:p02689] Rooted 61.2707 63.3571 1.03405
proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062] Measured 6112.4 6540.73 1.07008
1638 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 9895.77 9248.18 1.07002
growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] Squared 12067.6 13362.6 1.10731
kelch-like protein 8. [swissprot;acc:q9p2g9] Rooted 61.2707 63.3571 1.03405
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] Ranked 220.686 217.481 1.01474
1639 growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522] Squared 12067.6 13362.6 1.10731
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Rooted 61.2707 63.3571 1.03405
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Measured 5939.71 6354.79 1.06988
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Ranked 194.516 197.364 1.01464
1640 adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] Measured 7444.28 7964 1.06981
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Rooted 61.2707 63.3571 1.03405
hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235] Squared 12067.6 13362.6 1.10731
hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775] Ranked 194.516 197.364 1.01464
1641 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] Measured 5782.92 6186.39 1.06977
beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] Rooted 61.2707 63.3571 1.03405
growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293] Squared 12067.6 13362.6 1.10731
proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070] Ranked 218.167 215.034 1.01457
1642 40s ribosomal protein s7 (s8). [swissprot;acc:p23821] Measured 5782.92 6186.39 1.06977
doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] Squared 31032.5 34359.4 1.10721
fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Rooted 61.2707 63.3571 1.03405
m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] Ranked 260.269 256.531 1.01457
1643 26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805] Measured 5782.92 6186.39 1.06977
myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] Ranked 194.476 197.305 1.01455
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Squared 24729.7 27380.6 1.10719
retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329] Rooted 61.2707 63.3571 1.03405
1644 26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527] Squared 27191.5 30104.4 1.10713
apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114] Measured 5782.92 6186.39 1.06977
indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] Rooted 61.2707 63.3571 1.03405
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Ranked 217.256 214.149 1.01451
1645 prefoldin subunit 1. [swissprot;acc:o60925]
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Measured 6079.19 6503.12 1.06973
rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873] Squared 26883.9 29760.1 1.10699
s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] Rooted 64.5909 66.7876 1.03401
1646 atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] Squared 26883.9 29760.1 1.10699
molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Measured 6079.19 6503.12 1.06973
protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] Rooted 65.3639 67.5862 1.034
secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] Ranked 217.256 214.149 1.01451
1647 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Measured 6079.19 6503.12 1.06973

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/