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.


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 Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5408 to 5457 of 77072 in total
Rank
description
Value Type
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
169 zinc finger protein zfp6 (fragment). [sptrembl;acc:q92967] Rooted Subtracted Low confidence 0 45.3745 40.7828 4.5917
170 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Squared 1 54860.1 49344.1 5516
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Measured High confidence 0 668 475 193
amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Divided Low confidence 1 6131.26 6633.65 1.08194
b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Squared Subtracted High confidence 69165 52991.7 16173.3
b-lymphocyte activation-related protein. [sptrembl;acc:q96pn3] Ranked Divided Low confidence 0 4241.64 4837.61 1.1405
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Rooted High confidence 1 53.4993 45.9227 1.16499
calcyphosine. [swissprot;acc:q13938] Squared 0 175.528 276.854 1.57726
contactin associated protein-like 3 precursor (cell recognition molecule caspr3). [swissprot;acc:q9bz76] Subtracted Low confidence 17960.1 16641 1319.1
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Divided High confidence 1 96730.5 69286.7 1.39609
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Measured Low confidence 0 915.62 1122.57 1.22602
double-stranded rna-specific editase 1 (ec 3.5.-.-) (dsrna adenosine deaminase) (rna editing deaminase 1) (rna editing enzyme 1). [swissprot;acc:p78563] Rooted 17.1464 19.7737 1.15323
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Ranked Subtracted 10017.1 11477.1 1460
huntingtin interacting protein c. [refseq;acc:nm_012272] High confidence 1 227.971 200.417 27.554
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Measured 4247.86 5941.88 1694.02
inad-like protein isoform 3; pdz domain protein (drosophila inad-like); protein associated to tight junctions; pals1-associated tight junction protein; inactivation no after-potential d-like protein. [refseq;acc:nm_005799] Squared Divided Low confidence 67882.7 60913.7 1.11441
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Ranked High confidence 0 11364 12941 1.13877
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Rooted Subtracted 9.13761 12.1722 3.03459
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Measured Divided 1 23693.7 18263 1.29736
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Subtracted Low confidence 0 364 0 364
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Squared Divided 232467 160184 1.45125
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Ranked High confidence 1 227.199 192.715 1.17894
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Rooted Low confidence 70.7428 75.3259 1.06479
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Subtracted High confidence 55.6161 66.7332 11.1171
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Measured Low confidence 8973.23 9597.94 624.71
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Ranked Divided 216.783 205.066 1.05714
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Squared Subtracted High confidence 0 6777.96 6288.98 488.98
serpin b11. [swissprot;acc:q96p15] Rooted Divided 6.48074 7.48331 1.1547
striatin. [swissprot;acc:o43815] Subtracted Low confidence 1 66.4354 70.987 4.5516
t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] Ranked High confidence 0 12715.9 11333.2 1382.7
vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] Low confidence 1 202.698 191.393 11.305
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Measured Divided High confidence 0 112.666 141.702 1.25772
zinc finger protein 8 (zinc finger protein hf.18) (fragment). [swissprot;acc:p17098] Rooted Subtracted Low confidence 45.3729 40.7812 4.5917
171 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Measured Divided 222.779 181.734 1.22585
alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Ranked Subtracted High confidence 9875.43 11256.8 1381.37
alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] Squared Low confidence 9975.62 11288.3 1312.68
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Ranked 5029 6438 1409
atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] Measured High confidence 594 402 192
bet3 homolog. [swissprot;acc:o43617] Low confidence 1 8749.42 9372.33 622.91
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Squared Divided High confidence 96602.7 69211.2 1.39577
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Rooted Subtracted Low confidence 98.0366 93.4864 4.5502
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Divided High confidence 0 6.48074 7.48331 1.1547
defender against cell death 1 (dad-1). [swissprot;acc:p46966] Ranked Subtracted Low confidence 1 197.99 186.913 11.077
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Measured High confidence 4117.67 5801.04 1683.37
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Rooted 0 30.7397 27.7265 3.0132
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Ranked Divided Low confidence 1 219.889 208.064 1.05683
germ cell-less. [refseq;acc:nm_022471] Squared Subtracted High confidence 0 3567.33 3084.18 483.15
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Rooted Divided Low confidence 1 96.9641 103.242 1.06474
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] High confidence 61.6639 71.7355 1.16333
lamin b2. [swissprot;acc:q03252] Ranked 0 12135.4 13802 1.13733

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/