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.

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 Interaction Map Network Comparison Type Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 101 to 150 of 473 in total

Value Type: Measured
Interaction Map: High confidence
Network Comparison Type: Subtracted
Filtered: 1
red: 0
green: 0
network\_comparison: 0

\def\wcA{0.33333333333333\textwidth}
\def\wcB{0.33333333333333\textwidth}
\begin{longtable}{|c|c|}
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
description\vspace{3pt}}\\
\hline
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2856\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
high mobility group protein 2 (hmg-2). [source:swissprot;acc:p26583]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2857\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
protein kinase c, delta type (ec 2.7.1.-) (npkc-delta). [source:swissprot;acc:q05655]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2858\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
tyrosine-protein kinase ryk precursor (ec 2.7.1.112). [source:swissprot;acc:p34925]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2859\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homeobox protein nkx-6.1. [source:swissprot;acc:p78426]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2860\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
importin 9. [source:refseq;acc:nm\_018085]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2861\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
glucosamine-6-phosphate isomerase. [source:refseq;acc:nm\_138335]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2862\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
syndecan-3 (synd3). [source:swissprot;acc:o75056]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2863\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
high-glucose-regulated protein 8 (ny-ren-2 antigen). [source:swissprot;acc:q9y5a9]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2864\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mago nashi protein homolog. [source:swissprot;acc:p50606]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2865\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [source:swissprot;acc:p17542]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2866\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
syntaxin 5. [source:swissprot;acc:q13190]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2867\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [source:swissprot;acc:q9nzq3]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2868\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
eukaryotic initiation factor 4a-i (eif-4a-i) (eif4a-i). [source:swissprot;acc:p04765]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2869\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
phosphoribosyl pyrophosphate synthetase-associated protein 1 (prpp synthetase-associated protein 1) (39 kda phosphoribosypyrophosphate synthetase-associated protein) (pap39). [source:swissprot;acc:q14558]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2870\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
adaptor protein with pleckstrin homology and src homology 2 domains. [source:refseq;acc:nm\_020979]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2871\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
vps28 protein homolog. [source:swissprot;acc:q9uk41]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2872\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcriptional repressor nac1. [source:refseq;acc:nm\_052876]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2873\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
integrin beta-2 precursor (cell surface adhesion glycoproteins lfa- 1/cr3/p150,95 beta-subunit) (cd18) (complement receptor c3 beta- subunit). [source:swissprot;acc:p05107]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2874\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
protein c21orf2 (c21orf-humf09g8.5) (yf5/a2). [source:swissprot;acc:o43822]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2875\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
alpha crystallin a chain. [source:swissprot;acc:p02489]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2876\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
high-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9a (ec 3.1.4.17). [source:swissprot;acc:o76083]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2877\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [source:swissprot;acc:q01196]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2878\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nadh-ubiquinone oxidoreductase 49 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-49kd) (ci-49kd). [source:swissprot;acc:o75306]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2879\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
spir-2 protein (fragment). [source:sptrembl;acc:q8wwl2]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2880\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [source:refseq;acc:nm\_015650]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2881\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [source:refseq;acc:nm\_130386]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2882\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [source:swissprot;acc:p47989]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2883\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
pantothenate kinase 4 (ec 2.7.1.33) (pantothenic acid kinase 4) (hpank4). [source:swissprot;acc:q9nve7]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2884\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [source:swissprot;acc:q9hbh1]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2885\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [source:swissprot;acc:p23786]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2886\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
complement component c8 alpha chain precursor. [source:swissprot;acc:p07357]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2887\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mothers against decapentaplegic homolog interacting protein (madh-interacting protein) (smad anchor for receptor activation) (receptor activation anchor) (hsara) (novel serine protease) (nsp). [source:swissprot;acc:o95405]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2888\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [source:swissprot;acc:q14240]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2889\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [source:swissprot;acc:p06133]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2890\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [source:swissprot;acc:q9uff9]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2891\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
putative mitochondrial solute carrier; hypothetical protein npd016; putative mitochondrial solute carrier. [source:refseq;acc:nm\_031212]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2892\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [source:refseq;acc:nm\_015076]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2893\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [source:swissprot;acc:p18859]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2894\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription initiation factor iie, alpha subunit (tfiie-alpha) (general transcription factor iie 56 kda subunit). [source:swissprot;acc:p29083]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2895\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [source:swissprot;acc:p21108]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2896\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
bone morphogenetic protein 6 precursor (bmp-6). [source:swissprot;acc:p22004]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2897\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
serine/threonine kinase 38 like. [source:refseq;acc:nm\_015000]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2898\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
likely ortholog of mouse c-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13; c-type lectin 13; likely ortholog of rat kupffer cell c-type lectin receptor. [source:refseq;acc:nm\_173535]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2899\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
sparc-like protein 1 precursor (high endothelial venule protein) (hevin) (mast 9). [source:swissprot;acc:q14515]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2900\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
schwannomin interacting protein 1. [source:refseq;acc:nm\_014575]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2901\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [source:swissprot;acc:q9y6m4]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2902\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ubiquitin protein ligase. [source:refseq;acc:nm\_130466]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2903\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
protein transport protein sec24d (sec24-related protein d). [source:swissprot;acc:o94855]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2904\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [source:swissprot;acc:q03393]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2905\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [source:swissprot;acc:p05556]\vspace{3pt}}\\\hline
nd{longtable}

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/