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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 262 to 311 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
131 SON son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Divided 294.053 242.562 1.21228
132 NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Subtracted 229.406 196.695 32.711
TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Divided 350 290 1.2069
133 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 226.887 194.72 32.167
TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Divided 350 290 1.2069
134 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Subtracted 226.884 194.79 32.094
DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Divided 350 290 1.2069
135 CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]
FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted 263.215 231.407 31.808
136 CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Divided 350 290 1.2069
FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 263.215 231.407 31.808
137 FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 263.191 231.394 31.797
RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Divided 350 290 1.2069
138 PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 194.372 234.204 1.20493
TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Subtracted 174.667 205.556 30.889
139 APBA1 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] Divided 271.752 225.68 1.20415
CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Subtracted 287.41 256.835 30.575
140 NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 228.306 198.011 30.295
RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Divided 59 49 1.20408
141 COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Subtracted 239.991 269.238 29.247
RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Divided 59 49 1.20408
142 RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]
THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] Subtracted 239.99 269.234 29.244
143 ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Divided 59 49 1.20408
SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Subtracted 240.133 211.382 28.751
144 CSRP1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 239.35 267.915 28.565
KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Divided 265.686 319.651 1.20312
145 KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 265.639 319.546 1.20293
SHCBP1 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Subtracted 239.336 267.881 28.545
146 CSRP2 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 267.879 28.543
KCNIP2 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] Divided 265.632 319.531 1.20291
147 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 50.7983 42.3003 1.2009
CSRP3 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Subtracted 239.32 267.842 28.522
148 FLNB 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] 226.582 198.444 28.138
UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Divided 296.677 247.559 1.19841
149 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 142 170 1.19718
REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Subtracted 226.582 198.444 28.138
150 MYO5B myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Divided 55 46 1.19565
PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Subtracted 226.582 198.444 28.138
151 MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Divided 55 46 1.19565
PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Subtracted 226.582 198.444 28.138
152 no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Divided 55 46 1.19565
SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Subtracted 226.582 198.444 28.138
153 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
RBM15B chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Divided 249.663 298.263 1.19466
154 MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Subtracted 227.491 199.458 28.033
RGS19 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Divided 249.663 298.263 1.19466
155 MSI1 musashi 1. [refseq;acc:nm_002442] Subtracted 227.491 199.458 28.033
RBM15 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Divided 249.663 298.263 1.19466
156 RGS20 regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]

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
- Hugo is the HGNC identifier if it exists
- 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/