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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 475 to 524 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
red
green
network_comparison
60 GBE1 Measured 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Divided 4489.19 2765.82 1.6231
GNG8 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 266.864 336.184 1.25976
MAGEA6 Squared melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 219048 129762 1.68808
MAGEC1 Rooted melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Subtracted 137.446 120.823 16.623
PPP1R2 Squared protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 192904 126167 66737
SON Rooted 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 35.6294 49.8119 1.39806
61 ARRB2 Measured beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Subtracted 6475.5 10307.5 3832
GNG5 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Divided 266.864 336.182 1.25975
KCND3 potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Subtracted 269.248 327.642 58.394
KCNIP1 Rooted kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Divided 43.4291 31.7159 1.36932
MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Subtracted 137.446 120.823 16.623
NDN Squared necdin. [swissprot;acc:q99608] Divided 219048 129762 1.68808
PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Subtracted 192779 126095 66684
PYGB Measured glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Divided 4489.19 2765.82 1.6231
62 no value Rooted melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Subtracted 137.446 120.823 16.623
ARRB1 Measured beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 6475.5 10307.5 3832
GNG10 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Divided 266.865 336.181 1.25974
KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Subtracted 269.23 327.601 58.371
KCNIP4 Rooted potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Divided 43.4519 31.7522 1.36847
MAGED1 Squared melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 219048 129762 1.68808
PYGL Measured glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 4489.19 2765.82 1.6231
RRS1 Squared ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Subtracted 189976 124480 65496
63 no value Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Divided 266.865 336.178 1.25973
KCNIP2 Rooted 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] 43.4554 31.7576 1.36835
MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Subtracted 137.446 120.823 16.623
MAGEF1 Squared melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Divided 219048 129762 1.68808
MYO15A Measured myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 4489.19 2765.82 1.6231
NFYC Ranked 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] Subtracted 260.532 204.309 56.223
PPP1CA Squared serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 189976 124480 65496
SPATA6 Measured spermatogenesis associated 6. [refseq;acc:nm_019073] 6475.5 10307.5 3832
64 AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
ATG4A Squared cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 144940 81169.7 63770.3
GBE1 Rooted 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Divided 63.8686 47.2654 1.35128
GNG11 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 266.868 336.159 1.25965
MAGEB4 Rooted melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Subtracted 137.446 120.823 16.623
MAGEB6B Squared melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided 219048 129762 1.68808
NFYA Ranked 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] Subtracted 260.532 204.309 56.223
PYGM Measured glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 4489.19 2765.82 1.6231
65 no value Ranked serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Subtracted 187.457 243.678 56.221
Squared melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 219048 129762 1.68808
CSTF3 Measured cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Subtracted 22515.5 18702.6 3812.9
GNAQ Ranked guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Divided 267.136 336.077 1.25807
MAGED2 Rooted melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Subtracted 137.446 120.823 16.623
MAP1LC3B Squared microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 144912 81155 63757
NEURL Measured neuralized-like. [refseq;acc:nm_004210] Divided 1657.68 2690.25 1.6229
PYGB Rooted glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 63.8686 47.2654 1.35128
66 ARAF Measured a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Subtracted 17757.5 14008 3749.5
GNA11 Ranked guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Divided 267.136 336.077 1.25807
MAGEA9 Squared melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 219048 129762 1.68808
MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Subtracted 144911 81154.7 63756.3

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/