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 1075 to 1124 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
Interaction Map
red
green
network_comparison
135 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Rooted Low confidence 64.1536 68.7605 1.07181
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Ranked High confidence 350 290 1.2069
high-mobility group 20a. [refseq;acc:nm_018200] Measured Low confidence 7248.24 7916.96 1.09226
methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Squared 63248.6 71782.7 1.13493
neuronal protein np25. [swissprot;acc:q9ui15] Ranked 218.66 205.57 1.06368
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Squared High confidence 81888.8 56306.5 1.45434
136 adiponectin receptor 2. [refseq;acc:nm_024551] Rooted 41.8357 50.6469 1.21061
brain protein 44. [swissprot;acc:o95563] Squared Low confidence 62640.6 71038.3 1.13406
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Ranked High confidence 350 290 1.2069
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Low confidence 202.996 190.854 1.06362
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] Measured High confidence 3620.77 4763.34 1.31556
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Low confidence 7020.48 7667.34 1.09214
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Rooted 72.3705 77.5037 1.07093
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Squared High confidence 81888.8 56306.5 1.45434
137 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] Measured 3620.77 4763.34 1.31556
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Squared 81606.8 56215.8 1.45167
musashi 2 isoform a. [refseq;acc:nm_138962] Rooted 54.9787 66.2416 1.20486
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Low confidence 69.4253 64.8315 1.07086
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Ranked High confidence 350 290 1.2069
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Measured Low confidence 6139.6 6699.58 1.09121
testican-3 precursor. [swissprot;acc:q9bq16] Ranked 220.395 234.389 1.0635
zinc finger protein 216. [swissprot;acc:o76080] Squared 79152.9 69833.1 1.13346
138 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Measured 6709 7313.38 1.09008
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 2755.15 2094.3 1.31555
musashi 1. [refseq;acc:nm_002442] Rooted 54.9787 66.2416 1.20486
protein associated with prk1. [refseq;acc:nm_019006] Squared Low confidence 79152.9 69833.1 1.13346
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] High confidence 468498 322755 1.45156
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Rooted Low confidence 65.9611 70.6132 1.07053
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Ranked High confidence 194.372 234.204 1.20493
transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Low confidence 218.36 205.4 1.0631
139 60s ribosomal protein l37a. [swissprot;acc:p12751] Measured 5762.4 6277.91 1.08946
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] Ranked High confidence 271.752 225.68 1.20415
g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Squared 81592.1 56211.1 1.45153
nuclear protein ukp68. [refseq;acc:nm_024824] Rooted 54.9787 66.2416 1.20486
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Measured 2759.61 2099.49 1.31442
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Squared Low confidence 60231.9 53140.7 1.13344
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Rooted 65.9882 70.626 1.07028
testican-1 precursor (spock protein). [swissprot;acc:q08629] Ranked 220.254 234.111 1.06291
140 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Squared High confidence 81527.6 56190.6 1.45091
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Rooted 55.6161 66.7332 1.19989
kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Measured 2760.28 2100.27 1.31425
monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375] Squared Low confidence 62486.3 70725.6 1.13186
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Rooted 69.4376 64.8818 1.07022
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Ranked High confidence 59 49 1.20408
testican-2 precursor. [swissprot;acc:q92563] Low confidence 220.222 234.047 1.06278
ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Measured 7628.44 8310.74 1.08944
141 brachyury protein (t protein). [swissprot;acc:o15178] 6171.76 6720.84 1.08897
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Rooted 65.6112 70.2066 1.07004
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Squared High confidence 81520.8 56188.5 1.45084
monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985] Low confidence 62462.2 70689.7 1.13172

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/