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 Network Comparison Type Gene Value Type description Interaction Map green red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
Network Comparison Type
description
Interaction Map
green
red
network_comparison
126 Divided cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] High confidence 18164.9 24250 1.33499
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Low confidence 10318.5 11285.3 1.0937
Subtracted lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 7884.98 7098.44 786.54
rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 2394.5 450.5 1944
127 Divided melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Low confidence 10318.5 11285.3 1.0937
transcription factor jun-d. [swissprot;acc:p17535] High confidence 7523.39 5638.2 1.33436
Subtracted mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Low confidence 10870.9 10087.8 783.1
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 2394.5 450.5 1944
128 Divided luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 5810.82 4355.61 1.3341
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Low confidence 10318.5 11285.3 1.0937
Subtracted t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] High confidence 12944.2 11004.2 1940
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Low confidence 8046.29 7263.76 782.53
129 Divided luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] High confidence 5811.49 4358.13 1.33348
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Low confidence 10318.5 11285.3 1.0937
Subtracted prohibitin. [swissprot;acc:p35232] 11422.5 10642 780.5
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] High confidence 13346.9 15274.9 1928
130 Divided forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 2978.53 2234.68 1.33287
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] Low confidence 10318.5 11285.3 1.0937
Subtracted p66 alpha. [refseq;acc:nm_017660] High confidence 10911.1 12839 1927.9
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Low confidence 4614.87 3840.85 774.02
131 Divided forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] High confidence 2978.57 2234.73 1.33285
trophinin. [swissprot;acc:q12816] Low confidence 10318.5 11285.3 1.0937
Subtracted transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] 8391.85 7624.8 767.05
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] High confidence 10911.1 12839 1927.9
132 Divided dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] Low confidence 5441.83 5948.88 1.09318
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] High confidence 2980.35 2236.61 1.33253
Subtracted segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Low confidence 7794.8 7030.67 764.13
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] High confidence 10911.1 12839 1927.9
133 Divided gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 17580.4 23421.5 1.33225
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Low confidence 7662.77 7013 1.09265
Subtracted cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] High confidence 10887.2 12798.9 1911.7
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Low confidence 7797.14 7034.43 762.71
134 Divided ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 7286.66 6670.21 1.09242
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] High confidence 16426.1 21785.2 1.32626
Subtracted g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 10886 12796.8 1910.8
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Low confidence 7809.38 7054.1 755.28
135 Divided apg3p; pc3-96 protein. [refseq;acc:nm_022488] High confidence 16426.1 21785.2 1.32626
high-mobility group 20a. [refseq;acc:nm_018200] Low confidence 7916.96 7248.24 1.09226
Subtracted alpha-aminoadipate aminotransferase; l-kynurenine/alpha-aminoadipate aminotransferase; kynurenine aminotransferase ii. [refseq;acc:nm_016228] 10741.3 9986.51 754.79
transcription factor jun-b. [swissprot;acc:p17275] High confidence 7488.4 5579.18 1909.22
136 Divided nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 4763.34 3620.77 1.31556
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Low confidence 7667.34 7020.48 1.09214
Subtracted cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] High confidence 10880.5 12787.6 1907.1
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Low confidence 10650.5 9896.39 754.11
137 Divided ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] High confidence 4763.34 3620.77 1.31556
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Low confidence 6699.58 6139.6 1.09121
Subtracted g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] High confidence 10879.9 12786.6 1906.7
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Low confidence 8050.82 7297.57 753.25
138 Divided glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 7313.38 6709 1.09008
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 2094.3 2755.15 1.31555

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/