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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2680 to 2729 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
168 lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] Squared Divided 0 338.863 213.584 1.58656
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Measured 1 23693.7 18263 1.29736
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Rooted 0 43.2078 37.3703 1.15621
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Squared 1 173408 242989 1.40126
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Rooted Subtracted 55.6161 66.7332 11.1171
serpin b12. [swissprot;acc:q96p63] Measured 0 199.549 5.56738 193.982
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 18.9056 15.8624 3.0432
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Divided 1 56.3709 65.8949 1.16895
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Measured 0 334.012 420.355 1.2585
169 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Ranked 9875.43 11256.8 1.13988
apg3p; pc3-96 protein. [refseq;acc:nm_022488] 1 82.5916 98.0548 1.18722
cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Rooted 62.762 53.7761 1.1671
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Ranked Subtracted 312 284 28
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Measured 4245.52 5942.75 1697.23
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Divided 0 244 194 1.25773
Squared 14.0914 8.90793 1.58189
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Measured Subtracted 199.249 5.71669 193.532
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Rooted 25.0015 28.0435 3.042
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Divided 6.48074 7.48331 1.1547
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Measured 1 23693.7 18263 1.29736
pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Squared Subtracted 69165 52991.7 16173.3
pp3111 protein. [refseq;acc:nm_022156] Ranked 0 6185 7603 1418
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Rooted 1 55.6161 66.7332 11.1171
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Squared 0 1914.2 1419.67 494.53
symplekin. [swissprot;acc:q92797] Divided 1 124118 88668.8 1.39979
170 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Measured Subtracted 0 668 475 193
b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Squared 1 69165 52991.7 16173.3
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Rooted Divided 53.4993 45.9227 1.16499
calcyphosine. [swissprot;acc:q13938] Squared 0 175.528 276.854 1.57726
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 1 96730.5 69286.7 1.39609
huntingtin interacting protein c. [refseq;acc:nm_012272] Ranked Subtracted 227.971 200.417 27.554
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Measured 4247.86 5941.88 1694.02
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Ranked Divided 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
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Ranked 227.199 192.715 1.17894
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Rooted Subtracted 55.6161 66.7332 11.1171
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Squared 0 6777.96 6288.98 488.98
serpin b11. [swissprot;acc:q96p15] Rooted Divided 6.48074 7.48331 1.1547
t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] Ranked Subtracted 12715.9 11333.2 1382.7
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Measured Divided 112.666 141.702 1.25772
171 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Ranked Subtracted 9875.43 11256.8 1381.37
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 594 402 192
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Squared Divided 1 96602.7 69211.2 1.39577
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Rooted 0 6.48074 7.48331 1.1547
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Measured Subtracted 1 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
germ cell-less. [refseq;acc:nm_022471] Squared 3567.33 3084.18 483.15
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Rooted Divided 1 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/