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 Interaction Map Network Comparison Type green Filtered red network_comparison
Results: HTML CSV LaTeX Showing element 1101 to 1150 of 19268 in total
Value Type  : Ranked
Rank
description
Interaction Map
Network Comparison Type
green
Filtered
red
network_comparison
138 serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] High confidence Divided 234.204 1 194.372 1.20493
serpin b11. [swissprot;acc:q96p15] Subtracted 15123 0 16853 1730
transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Low confidence Divided 205.4 1 218.36 1.0631
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] 7516 0 8730 1.16152
139 alpha crystallin a chain. [swissprot;acc:p02489] High confidence 13972.2 16372.4 1.17178
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] 225.68 1 271.752 1.20415
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Subtracted 256.835 287.41 30.575
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 15123 0 16853 1730
dnaj homolog subfamily c member 8 (splicing protein spf31) (hspc315). [swissprot;acc:o75937] Low confidence 207.417 1 219.838 12.421
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Divided 10962.4 0 12716.5 1.16001
testican-1 precursor (spock protein). [swissprot;acc:q08629] 234.111 1 220.254 1.06291
tubulin beta-4q chain. [swissprot;acc:q99867] Subtracted 14500.6 0 12800.9 1699.7
140 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] High confidence 198.011 1 228.306 30.295
beta-tubulin 4q. [sptrembl;acc:q8wz78] Low confidence 14497.6 0 12807 1690.6
c3hc4-type zinc finger protein; likely ortholog of mouse dioxin inducible factor 3. [refseq;acc:nm_024835] 207.417 1 219.838 12.421
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] High confidence 16802.1 0 15081.8 1720.3
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] Divided 14027.1 16411.9 1.17001
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 49 1 59 1.20408
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Low confidence 7533.54 0 6520.34 1.15539
testican-2 precursor. [swissprot;acc:q92563] 234.047 1 220.222 1.06278
141 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] High confidence Subtracted 269.238 239.991 29.247
endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7] Low confidence 198.732 211.056 12.324
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] High confidence Divided 8991.19 0 7690.02 1.1692
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 49 1 59 1.20408
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Low confidence 206.52 219.344 1.0621
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] High confidence Subtracted 11119.7 0 9411.34 1708.36
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] Low confidence Divided 15652 18079 1.15506
tubulin beta-4 chain (tubulin beta-iii). [swissprot;acc:q13509] Subtracted 14496.9 12808.5 1688.4
142 endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7] Divided 198.732 1 211.056 1.06201
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted 12.324
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] High confidence Divided 49 59 1.20408
thrombospondin 3 precursor. [swissprot;acc:p49746] Subtracted 269.234 239.99 29.244
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Low confidence 11039.5 0 9351.39 1688.11
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] High confidence 18296 16614 1682
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Divided 7026.41 8214.41 1.16908
zinc finger protein 183-like 1. [refseq;acc:nm_178861] Low confidence 12382.9 10720.7 1.15505
143 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] High confidence 49 1 59 1.20408
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Low confidence 16782.2 0 14529.8 1.15502
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] High confidence 13005.3 11124.8 1.16904
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Low confidence Subtracted 198.732 1 211.056 12.324
metaxin 1. [swissprot;acc:q13505] 12622.6 0 10935 1687.6
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] High confidence 7868 9545 1677
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Low confidence Divided 198.732 1 211.056 1.06201
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] High confidence Subtracted 211.382 240.133 28.751
144 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 267.915 239.35 28.565
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Divided 13000.1 0 11123.4 1.16872
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Low confidence 198.732 1 211.056 1.06201
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 319.651 265.686 1.20312
l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338] Low confidence 16094.8 0 18586.3 1.1548
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted 198.732 1 211.056 12.324

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/