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 425 to 474 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
107 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Divided 1 4266.04 5843.51 1.36977
60s ribosomal protein l7. [swissprot;acc:p18124] Subtracted 0 1915.27 2206.07 290.8
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Divided 326.677 472.605 1.4467
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Subtracted 1 14229.2 16780.7 2551.5
108 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] Divided 0 292 421 1.44178
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] 1 4366.44 5899.76 1.35116
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Subtracted 0 482.426 192.295 290.131
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 1 14021.4 11523 2498.4
109 44050 protein. [refseq;acc:nm_178832] 17385.9 14889.2 2496.7
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Divided 0 100 144 1.44
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 1 4366.44 5899.76 1.35116
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Subtracted 0 934.726 1222.89 288.164
110 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 528.5 816.5 288
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] 1 17385.9 14889.2 2496.7
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Divided 4366.44 5899.76 1.35116
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 0 1833 2637 1.43863
111 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 1 4366.44 5899.76 1.35116
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 0 2965.5 2063 1.43747
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Subtracted 10247.8 10535 287.2
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 1 12365.2 14824.9 2459.7
112 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 11757.8 9352.11 2405.69
lats homolog 1. [refseq;acc:nm_004690] Divided 0 160 112.25 1.42539
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Subtracted 1095.42 812.166 283.254
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Divided 1 4366.44 5899.76 1.35116
113 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Subtracted 4800.81 7132.71 2331.9
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 4366.44 5899.76 1.35116
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] 0 160 112.25 1.42539
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Subtracted 3117.17 2833.94 283.23
114 60s ribosomal protein l37a. [swissprot;acc:p12751] 305.45 26.1599 279.29
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 1 13768.2 11466 2302.2
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Divided 0 671.769 472.945 1.4204
huntingtin interacting protein c. [refseq;acc:nm_012272] 1 4300.47 5807.72 1.35048
115 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Subtracted 0 305.45 26.1599 279.29
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided 1 21185 28492 1.34491
pnas-18. [sptrembl;acc:q9bzu3] Subtracted 13680.5 11409.6 2270.9
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Divided 0 385 543 1.41039
116 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 668 475 1.40632
cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Subtracted 1382.5 1107 275.5
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Divided 1 21185 28492 1.34491
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Subtracted 13261.9 11017.8 2244.1
117 ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 0 1161.88 891.114 270.766
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 1 9276.47 7090.37 2186.1
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Divided 21185 28492 1.34491
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 0 170.5 122 1.39754
118 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Subtracted 1 9275.1 7089.65 2185.45
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 0 324.442 593.094 268.652
methyltransferase like 2. [refseq;acc:nm_018396] Divided 31 43 1.3871
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 1 21185 28492 1.34491
119 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Subtracted 12998.5 15138.2 2139.7
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Divided 0 633.85 460.2 1.37734

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/