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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 1963 to 2012 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
green
red
network_comparison
491 pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Subtracted 0 2411.78 2410.35 1.43
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] 1 7909.27 7067.46 841.81
492 3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] Divided 0 5046.33 5038.33 1.00159
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 1 6842.76 5979.94 1.14429
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Subtracted 0 249.857 250.419 0.562
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 1 7007.7 6167.93 839.77
493 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Divided 6842.78 5979.95 1.14429
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] 0 2411.78 2410.35 1.00059
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Subtracted 249.857 250.419 0.562
494 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Divided 1 6842.72 5979.93 1.14428
histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261] 0 0.00001 0.00001 1
Subtracted 0 0 0
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] 1 7007.7 6167.93 839.77
495 histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001] Divided 0 0.00001 0.00001 1
Subtracted 0 0 0
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] 1 7007.7 6167.93 839.77
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Divided 12363.6 10804.7 1.14428
496 inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Subtracted 7007.7 6167.93 839.77
mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932] Divided 0 0.00001 0.00001 1
Subtracted 0 0 0
nostrin. [refseq;acc:nm_052946] Divided 1 4093.05 4682.87 1.1441
497 eap30 subunit of ell complex. [refseq;acc:nm_007241]
histone h2a; h2a histone family, member r. [refseq;acc:nm_170745] 0 0.00001 0.00001 1
Subtracted 0 0 0
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 1 5554.38 4714.85 839.53
498 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Divided 4093.05 4682.87 1.1441
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Subtracted 7766.54 6933.17 833.37
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Divided 0 0.00001 0.00001 1
Subtracted 0 0 0
499 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Divided 1 4093.05 4682.87 1.1441
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 0 0.00001 0.00001 1
Subtracted 0 0 0
transcription factor btf3 homolog 3. [swissprot;acc:q13892] 1 7770.65 6938.22 832.43
500 gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Divided 4093.05 4682.87 1.1441
huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Subtracted 9902.6 10733.4 830.8
rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] Divided 0 0.00001 0.00001 1
Subtracted 0 0 0
501 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Divided 1 4093.05 4682.87 1.1441
goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Subtracted 9896.32 10725.6 829.28
h2a histone family, member j isoform 1. [refseq;acc:nm_018267] Divided 0 0.00001 0.00001 1
Subtracted 0 0 0
502 brca1 associated protein. [refseq;acc:nm_006768] Divided 0.00001 0.00001 1
Subtracted 0 0 0
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] 1 9891.08 10719 827.92
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Divided 7907.05 6913.6 1.1437
503 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Subtracted 7747.63 6920.69 826.94
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Divided 13277.9 15182.5 1.14344
504 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Subtracted 7747.65 6920.71 826.94
enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Divided 11511 10067.9 1.14334

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/