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 24676 to 24725 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
2583 hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] Measured Subtracted 3436.65 3531.96 95.31
polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Divided 3926.4 3857.88 1.01776
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Squared Subtracted 28128.8 28940.3 811.5
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Rooted 62.9549 63.4703 0.5154
transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] Squared Divided 31221.5 32578.2 1.04345
2584 deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] Measured 4180.32 4253.46 1.0175
dystrophin. [swissprot;acc:p11532] Ranked 213.422 213.75 1.00154
Subtracted 0.328
growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] Measured 3436.65 3531.96 95.31
insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47] Squared Divided 36431.8 34958.8 1.04214
serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] Rooted 59.5213 60.0364 1.00865
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Subtracted 62.9549 63.4703 0.5154
stromal interaction molecule 2 precursor. [swissprot;acc:q9p246] Squared 28128.8 28940.3 811.5
2585 angiomotin. [refseq;acc:nm_133265] Ranked Divided 213.422 213.75 1.00154
Subtracted 0.328
cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Rooted 62.955 63.4703 0.5153
growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522] Measured 3436.65 3531.96 95.31
neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] Rooted Divided 59.5205 60.0353 1.00865
protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] Squared 28228.7 29412.6 1.04194
rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] Measured 4180.32 4253.46 1.0175
serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286] Squared Subtracted 28128.8 28940.3 811.5
2586 activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] Rooted 59.5216 60.0368 0.5152
angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201] Ranked Divided 213.422 213.75 1.00154
Subtracted 0.328
hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235] Measured 3436.65 3531.96 95.31
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] Divided 4180.32 4253.46 1.0175
tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] Rooted 59.5189 60.0331 1.00864
wd repeat domain 26. [refseq;acc:nm_025160] Squared 32575.7 33907 1.04087
wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] Subtracted 28130.1 28941.4 811.3
2587 alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424] Ranked Divided 213.422 213.75 1.00154
Subtracted 0.328
dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] Rooted Divided 55.9762 55.5001 1.00858
growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293] Measured Subtracted 3436.65 3531.96 95.31
insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663] Squared Divided 36688.8 35252 1.04076
map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] Measured 4180.32 4253.46 1.0175
serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] Rooted Subtracted 59.5213 60.0364 0.5151
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Squared 20043.6 20854.9 811.3
2588 60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809] Ranked Divided 222.305 222.64 1.00151
hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] Measured Subtracted 7197.82 7291.66 93.84
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Rooted Divided 45.2905 44.9065 1.00855
meiotic recombination protein spo11. [swissprot;acc:q9y5k1] Measured 4180.32 4253.46 1.0175
paraspeckle protein 1. [refseq;acc:nm_018282] Rooted Subtracted 80.3509 79.8358 0.5151
polybromo 1. [refseq;acc:nm_018165] Ranked 220.02 219.696 0.324
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Squared 14393.2 13586.9 806.3
transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] Divided 34721.5 36133.4 1.04066
2589 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Measured 7181.3 7057.99 1.01747
dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] Subtracted 3803.04 3710.01 93.03
membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] Ranked Divided 212.74 212.422 1.0015
neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] Rooted Subtracted 59.5205 60.0353 0.5148
sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] Divided 62.9549 63.4703 1.00819

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/