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 268 to 317 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
134 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Divided 21785.2 16426.1 1.32626
135 apg3p; pc3-96 protein. [refseq;acc:nm_022488]
transcription factor jun-b. [swissprot;acc:p17275] Subtracted 5579.18 7488.4 1909.22
136 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 12787.6 10880.5 1907.1
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] Divided 3620.77 4763.34 1.31556
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]
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Subtracted 12786.6 10879.9 1906.7
138 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Divided 2755.15 2094.3 1.31555
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Subtracted 15182.5 13277.9 1904.6
139 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 12780.7 10876.4 1904.3
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Divided 2759.61 2099.49 1.31442
140 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Subtracted 2597.5 698.5 1899
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 2760.28 2100.27 1.31425
141 hbs1-like. [refseq;acc:nm_006620] Subtracted 2597.5 698.5 1899
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Divided 4405.4 5782.08 1.3125
142 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 9276.47 7090.37 1.30832
transcription factor jun-d. [swissprot;acc:p17535] Subtracted 5638.2 7523.39 1885.19
143 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Divided 9275.1 7089.65 1.30826
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Subtracted 15427.2 13572.8 1854.4
144 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 4133.47 5945.32 1811.85
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Divided 3349.9 4362.61 1.30231
145 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Subtracted 4136.36 5943.56 1807.2
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Divided 16771.5 12889.1 1.30122
146 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 11068 8508.5 1.30082
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Subtracted 2671 871 1800
147 protein x 0004. [refseq;acc:nm_016301]
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided 11068 8508.5 1.30082
148 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]
symplekin. [swissprot;acc:q92797] Subtracted 15213.4 13418.1 1795.3
149 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Divided 11068 8508.5 1.30082
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Subtracted 11736.6 13531.9 1795.3
150 protein hspc134 (protein cda04). [swissprot;acc:q9by43] Divided 11068 8508.5 1.30082
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted 4172.91 5954.48 1781.57
151 pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 14830.5 13050.3 1780.2
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Divided 4578.09 5939.91 1.29746
152 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] Subtracted 5136.78 6895.98 1759.2
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Divided 23693.7 18263 1.29736
153 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Subtracted 9035 7279.6 1755.4
154 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Divided 23693.7 18263 1.29736
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Subtracted 9035 7279.6 1755.4
155 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Divided 23693.7 18263 1.29736
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Subtracted 9035 7279.6 1755.4
156 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Divided 23693.7 18263 1.29736
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Subtracted 9035 7279.6 1755.4
157 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Divided 23693.7 18263 1.29736
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Subtracted 9035 7279.6 1755.4
158 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Divided 23693.7 18263 1.29736
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Subtracted 9035 7279.6 1755.4
159 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]

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/