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 1344 to 1393 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
168 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
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Measured 0 244 194 1.25773
Squared 14.0914 8.90793 1.58189
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Rooted 6.48074 7.48331 1.1547
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Measured 1 23693.7 18263 1.29736
symplekin. [swissprot;acc:q92797] Squared 124118 88668.8 1.39979
170 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Rooted 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
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Ranked 0 11364 12941 1.13877
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Measured 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
serpin b11. [swissprot;acc:q96p15] Rooted 0 6.48074 7.48331 1.1547
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Measured 112.666 141.702 1.25772
171 ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Squared 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
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 1 61.6639 71.7355 1.16333
lamin b2. [swissprot;acc:q03252] Ranked 0 12135.4 13802 1.13733
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Measured 1 23693.7 18263 1.29736
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Ranked 227.202 192.823 1.17829
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Squared 0 1592.06 2488.07 1.5628
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] Measured 112.666 141.702 1.25772
172 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Ranked 1 174.667 205.556 1.17685
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Squared 121579 87259.3 1.39331
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 0 47.4746 74.0536 1.55986
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Rooted 40.4536 35.073 1.15341
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 1 56.7592 65.9889 1.16261
trophinin. [swissprot;acc:q12816] Measured 23693.7 18263 1.29736
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] 0 112.666 141.702 1.25772
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Ranked 12225.7 13893.1 1.13638
173 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Rooted 1 145.551 168.796 1.1597
60s ribosomal protein l7. [swissprot;acc:p18124] 0 27.512 31.7228 1.15305
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Measured 1 4579.34 5940.64 1.29727
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 0 3265.25 4102.97 1.25656
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Squared 48.239 75.2348 1.55963
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] 1 82624.3 115061 1.39258
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Ranked 227.032 193.056 1.17599
suppressor of actin 1. [refseq;acc:nm_014016] 0 19088.1 16804.6 1.13589
174 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Rooted 15.8745 18.303 1.15298
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Squared 48.3438 75.3968 1.5596
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Ranked 1 335 286 1.17133
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Measured 0 488.43 612.604 1.25423
mad protein (max dimerizer). [swissprot;acc:q05195] 1 4455.95 5774.03 1.2958
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Rooted 145.551 168.796 1.1597
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Ranked 0 13248.5 11666.4 1.13561
sedlin. [swissprot;acc:o14582] Squared 1 112820 157033 1.39189
175 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Ranked 199.949 234.187 1.17123

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/