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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5808 to 5857 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
2904 PTS 6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393] Subtracted 0 0 0
2905 ITGB1 integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [swissprot;acc:p05556] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2906 TAOK2 thousand and one amino acid protein kinase. [refseq;acc:nm_004783] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2907 ALDOA fructose-bisphosphate aldolase a (ec 4.1.2.13) (muscle-type aldolase) (lung cancer antigen ny-lu-1). [swissprot;acc:p04075] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2908 CHEK1 serine/threonine-protein kinase chk1 (ec 2.7.1.-). [swissprot;acc:o14757] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2909 NKX6-2 nk6 transcription factor related, locus 2; nk homeobox family 6, b; glial and testis-specific homeobox protein; homeobox 6b. [refseq;acc:nm_177400] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2910 no value protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2911 COMMD3 bup protein. [refseq;acc:nm_012071] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2912 INPP5E inositol polyphosphate-5-phosphatase; phosphatidylinositol polyphosphate 5-phosphatase type iv; phosphatidylinositol (4,5) bisphosphate 5-phosphatase. [refseq;acc:nm_019892] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2913 AUH au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [refseq;acc:nm_001698] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2914 LACTB2 lactamase, beta 2. [refseq;acc:nm_016027] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2915 SLC25A37 mitochondrial solute carrier protein. [refseq;acc:nm_016612] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2916 PRPS1L1 ribose-phosphate pyrophosphokinase i (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase i) (ppribp) (prs-i). [swissprot;acc:p09329] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2917 CCT6A t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2918 GBAS nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2919 GLRA1 glycine receptor alpha-1 chain precursor (glycine receptor 48 kda subunit) (strychnine binding subunit). [swissprot;acc:p23415] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2920 GLRA3 glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2921 EAF2 ell-associated factor 2; uncharacterized bone marrow protein bm040; testosterone regulated apoptosis inducer and tumor suppressor. [refseq;acc:nm_018456] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2922 ALDH1L1 10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2923 TMEM4 transmembrane protein 4. [refseq;acc:nm_014255] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2924 RQCD1 rcd1 required for cell differentiation1 homolog; protein involved in sexual development; rcd1 (required for cell differentiation, s.pombe) homolog 1. [refseq;acc:nm_005444] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2925 RALB ras-related protein ral-b. [swissprot;acc:p11234] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2926 DUSP11 dual specificity protein phosphatase 11 (ec 3.1.3.48) (rna/rnp complex-intereracting phosphatase) (phosphatase that interacts with rna/rnp complex 1). [swissprot;acc:o75319] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2927 CIAO1 wd-repeat containing protein ciao 1. [swissprot;acc:o76071] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2928 no value calmodulin. [swissprot;acc:p02593] Divided 0.00001 0.00001 1
Subtracted 0 0 0
2929 LYST lysosomal trafficking regulator (beige homolog). [swissprot;acc:q99698] Divided 0.00001 0.00001 1

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
- Hugo is the HGNC identifier if it exists
- 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/