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 3258 to 3307 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
408 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Rooted Divided 49.9856 45.4432 1.09996
dok-like protein. [refseq;acc:nm_024872] Measured 6102.59 7081.46 1.1604
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Subtracted 1836.76 907.763 928.997
heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Ranked 237.109 254.667 17.558
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Rooted 59.6834 65.6741 5.9907
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Squared Divided 18995.7 23244.7 1.22368
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Subtracted 32193.3 37967.7 5774.4
409 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Measured Divided 6102.59 7081.46 1.1604
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Squared Subtracted 32192.8 37967.2 5774.4
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Measured 1836.76 907.774 928.986
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Rooted Divided 50.4409 45.8795 1.09942
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Subtracted 59.6834 65.6741 5.9907
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Ranked Divided 241.045 261.874 1.08641
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Subtracted 237.109 254.667 17.558
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Squared Divided 18995.6 23242.8 1.22359
410 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Measured Subtracted 6744.05 5815.13 928.92
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Squared Divided 19546.1 23881.6 1.22181
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Measured 6102.59 7081.46 1.1604
e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] Ranked Subtracted 237.109 254.667 17.558
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Squared 32192.5 37966.8 5774.3
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Rooted Divided 55.5489 50.535 1.09922
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Ranked 233.376 253.539 1.0864
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Rooted Subtracted 56.0061 61.9704 5.9643
411 60s ribosomal protein l18. [swissprot;acc:q07020] Ranked 237.109 254.667 17.558
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Squared 32192.5 37966.8 5774.3
guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Measured 1836.8 907.903 928.897
pp3111 protein. [refseq;acc:nm_022156] Rooted Divided 55.5489 50.535 1.09922
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Subtracted 58.6533 64.5958 5.9425
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Squared Divided 17861.2 21821.8 1.22174
tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] Ranked 233.376 253.539 1.0864
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Measured 6102.59 7081.46 1.1604
412 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Squared Subtracted 32192.6 37966.9 5774.3
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Measured 1836.81 907.978 928.832
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Divided 3594.31 4169.95 1.16015
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Rooted Subtracted 66.377 72.2842 5.9072
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Ranked 251.926 234.547 17.379
syntaxin 18. [swissprot;acc:q9p2w9] Rooted Divided 55.5489 50.535 1.09922
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Squared 19556 23891.8 1.22171
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] Ranked 240.788 261.416 1.08567
413 dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 240.913 261.45 1.08525
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Squared 19568.3 23904.6 1.2216
gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Subtracted 32192.8 37967.1 5774.3
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Measured 1836.81 907.978 928.832
rd protein. [swissprot;acc:p18615] Rooted Divided 55.5489 50.535 1.09922
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Subtracted 62.574 68.4128 5.8388
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Ranked 223.202 205.9 17.302
vav proto-oncogene. [swissprot;acc:p15498] Measured Divided 6644.99 7707.8 1.15994
414 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 6744.05 5815.13 1.15974
dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Squared 22109.6 26989.4 1.22071
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Rooted Subtracted 62.574 68.4128 5.8388

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/