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 12814 to 12863 of 77072 in total
Rank
description
Value Type
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
401 laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942] Rooted Subtracted Low confidence 0 8.7233 6.96791 1.75539
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Measured High confidence 1549.26 1522.06 27.2
mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932] Ranked 20914 20558 356
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 1 254.434 236.224 18.21
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Measured Divided 0 548.5 527.5 1.03981
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Squared Subtracted 1 28188.7 33982.7 5794
prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Divided Low confidence 45694.9 42750.3 1.06888
replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Ranked High confidence 207.908 226.218 1.08807
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Low confidence 0 11865.8 10971.5 1.08151
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Subtracted 1 200.057 192.938 7.119
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Rooted Divided High confidence 116.707 106.044 1.10055
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Squared Subtracted 0 12.5892 5.42219 7.16701
similar to peptidylprolyl isomerase a (cyclophilin a); cyclophilin-lc; cyclophilin homolog overexpressed in liver cancer; chromosome 1 amplified sequence 2. [refseq;acc:nm_178230] Rooted Divided Low confidence 21.5413 19.8385 1.08583
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Ranked 1 205.017 197.863 1.03616
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] High confidence 0 12305.9 11904.9 1.03368
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Measured Low confidence 1277.86 1410.56 1.10385
tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Rooted 1 75.7395 79.3703 1.04794
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Subtracted High confidence 55.9231 62.0565 6.1334
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] Ranked Low confidence 0 11212.4 11832.5 620.1
402 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Divided 11870.1 10979.9 1.08108
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Rooted High confidence 21.6987 22.4088 1.03273
adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] Ranked 10562.4 10918 1.03367
Subtracted 355.6
alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Measured Low confidence 1 8730.02 9159.19 429.17
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] High confidence 6230.94 7168.2 937.26
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] Squared Divided Low confidence 48608.6 45485.7 1.06866
brain protein 16. [refseq;acc:nm_016458] High confidence 0 2538.95 2371.77 1.07049
cab2. [refseq;acc:nm_033419] Subtracted 0 7.16592 7.16592
cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] Rooted Divided Low confidence 1 75.7377 79.3677 1.04793
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Subtracted 0 22.8868 24.6401 1.7533
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Squared 40468.6 40724.8 256.2
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Divided High confidence 1 39472 48393.1 1.22601
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Rooted 50.1918 55.2294 1.10037
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Squared Subtracted 28190.4 33984.1 5793.7
glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] Rooted Low confidence 70.0201 73.4927 3.4726
heat shock factor binding protein 1. [swissprot;acc:o75506] Squared Divided 0 6759.24 6076.24 1.11241
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Ranked Subtracted High confidence 1 231.802 249.983 18.181
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Rooted Divided Low confidence 0 21.5425 19.8515 1.08518
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Measured High confidence 1 5201.41 4479.76 1.16109
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Subtracted 0 12.6208 39.8063 27.1855
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] Ranked Low confidence 9431 8815 616
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Measured Divided High confidence 548.5 527.5 1.03981
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Rooted Subtracted 1 59.5128 65.604 6.0912
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Measured Divided Low confidence 0 1643.27 1812.61 1.10305
rab11-family interacting protein 4. [refseq;acc:nm_032932] Squared Subtracted 1 34469.6 37645.4 3175.8
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Ranked Divided High confidence 207.908 226.218 1.08807
sedlin. [swissprot;acc:o14582] Measured Subtracted Low confidence 0 181.896 299.876 117.98
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Divided 1 7934.21 8352.26 1.05269
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] Rooted Subtracted High confidence 0 17.8274 17.1002 0.7272
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Ranked Low confidence 1 210.292 203.181 7.111

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/