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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Hugo measured Gene Rank description expected final
Results: HTML CSV LaTeX Showing element 1758 to 1807 of 3206 in total
Hugo
measured
Rank
description
expected
final
MAGEA2B 0.0647324 3142 MELANOMA-ASSOCIATED ANTIGEN 2 (MAGE-2 ANTIGEN). [SWISSPROT;Acc:P43356] 0.990069 0.065381706
MAGEA4 0.0643408 3146 MELANOMA-ASSOCIATED ANTIGEN 12 (MAGE-12 ANTIGEN) (MAGE12F). [SWISSPROT;Acc:P43365] 0.98408 0.065381676
MAGEA6 0.0649797 3141 MELANOMA-ASSOCIATED ANTIGEN 6 (MAGE-6 ANTIGEN) (MAGE3B). [SWISSPROT;Acc:P43360] 0.993851 0.065381732
MAGEA8 0.0652476 3144 MELANOMA-ASSOCIATED ANTIGEN 8 (MAGE-8 ANTIGEN). [SWISSPROT;Acc:P43361] 0.997949 0.065381698
MAGEA9 0.0650415 3145 MELANOMA-ASSOCIATED ANTIGEN 9 (MAGE-9 ANTIGEN). [SWISSPROT;Acc:P43362] 0.994797 0.065381681
MAGEB10 0.066175 3136 1.01213 0.065381917
MAGEB18 0.0659071 3154 1.00804 0.065381433
MAGEB4 0.066752 3151 MELANOMA-ASSOCIATED ANTIGEN B1 (MAGE-B1 ANTIGEN) (MAGE-XP ANTIGEN) (DSS-AHC CRITICAL INTERVAL MAGE SUPERFAMILY 10) (DAM10). [SWISSPROT;Acc:P43366] 1.02096 0.065381602
MAGEB6B 0.0654743 3152 "MELANOMA ANTIGEN, FAMILY B, 6. [RefSeq;Acc:NM_173523]" 1.00142 0.065381458
MAGEC1 0.0649384 3150 MELANOMA-ASSOCIATED ANTIGEN C1 (MAGE-C1 ANTIGEN) (CANCER-TESTIS ANTIGEN CT7). [SWISSPROT;Acc:O60732] 0.993221 0.065381622
MAGED1 0.0662574 3134 MELANOMA-ASSOCIATED ANTIGEN D1 (MAGE-D1 ANTIGEN) (NEUROTROPHIN RECEPTOR-INTERACTING MAGE HOMOLOG) (PRO2292). [SWISSPROT;Acc:Q9Y5V3] 1.01339 0.065381936
MAGED2 0.0669169 3140 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] 1.02348 0.065381737
MAGED4 0.066175 3135 "MELANOMA ANTIGEN, FAMILY D, 4 ISOFORM 1; MAGE1 PROTEIN; MAGE-E1 PROTEIN; MAGED4 PROTEIN. [RefSeq;Acc:NM_030801]" 1.01213 0.065381917
MAGEE2 0.0645881 3143 HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA3. [RefSeq;Acc:NM_138703] 0.987862 0.065381703
MAGEF1 0.0698227 3155 MELANOMA-ASSOCIATED ANTIGEN F1 (MAGE-F1 ANTIGEN). [SWISSPROT;Acc:Q9HAY2] 1.06793 0.065381345
MAGI1 0.183128 296 BAI1-ASSOCIATED PROTEIN 1; WW DOMAIN-CONTAINING PROTEIN 3; ATROPHIN-1 INTERACTING PROTEIN 3. [RefSeq;Acc:NM_004742] 0.60884 0.300781815
MAGI2 0.227252 297 ATROPHIN-1 INTERACTING PROTEIN 1; ACTIVIN RECEPTOR INTERACTING PROTEIN 1; LIKELY ORTHOLOG OF MOUSE ACTIVIN RECEPTOR INTERACTING PROTEIN 1; ATROPHIN-1 INTERACTING PROTEIN A; MEMBRANE ASSOCIATED GUANYLATE KINASE 2; ACTIVIN RECEPTOR INTERACTING P. [Re 0.756337 0.300463947
MAN2B1 0.0662042 2906 "LYSOSOMAL ALPHA-MANNOSIDASE PRECURSOR (EC 3.2.1.24) (MANNOSIDASE, ALPHA B) (LYSOSOMAL ACID ALPHA-MANNOSIDASE) (LAMAN) (MANNOSIDASE ALPHA CLASS 2B MEMBER 1). [SWISSPROT;Acc:O00754]" 0.380173 0.174142298
MAP1LC3A 0.0764589 3065 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3A (MAP1A/MAP1B LC3 A) (MAP1A/1B LIGHT CHAIN 3 A). [SWISSPROT;Acc:Q9H492] 0.738297 0.103561168
MAP1LC3B 0.0670742 3066 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B (MAP1A/MAP1B LC3 B) (MAP1A/1B LIGHT CHAIN 3 B). [SWISSPROT;Acc:Q9GZQ8] 0.647682 0.103560389
MAP2K1 0.251342 570 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 (EC 2.7.1.-) (MAP KINASE KINASE 1) (MAPKK 1) (ERK ACTIVATOR KINASE 1) (MAPK/ERK KINASE 1) (MEK1). [SWISSPROT;Acc:Q02750] 0.928542 0.270684579
MAP2K2 569 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 2 (EC 2.7.1.-) (MAP KINASE KINASE 2) (MAPKK 2) (ERK ACTIVATOR KINASE 2) (MAPK/ERK KINASE 2) (MEK2). [SWISSPROT;Acc:P36507]
MAP2K3 0.127536 2616 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 3 (EC 2.7.1.-) (MAP KINASE KINASE 3) (MAPKK 3) (MAPK/ERK KINASE 3). [SWISSPROT;Acc:P46734] 0.605166 0.210745481
MAP2K4 0.10034 327 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 4 (EC 2.7.1.-) (MAP KINASE KINASE 4) (JNK ACTIVATING KINASE 1) (C-JUN N- TERMINAL KINASE KINASE 1) (JNKK) (SAPK/ERK KINASE 1) (SEK1). [SWISSPROT;Acc:P45985] 0.351521 0.285445251
MAP2K6 0.143053 2617 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 6 (EC 2.7.1.-) (MAP KINASE KINASE 6) (MAPKK 6) (MAPK/ERK KINASE 6) (SAPKK3). [SWISSPROT;Acc:P52564] 0.679075 0.210658617
MAP2K7 0.209195 480 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7 (EC 2.7.1.-) (MAP KINASE KINASE 7) (MAPKK 7) (MAPK/ERK KINASE 7) (JNK ACTIVATING KINASE 2) (C-JUN N-TERMINAL KINASE KINASE 2) (JNK KINASE 2) (JNKK 2). [SWISSPROT;Acc:O14733] 0.762639 0.274304094
MAP3K6 0.126275 695 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 6 (EC 2.7.1.-). [SWISSPROT;Acc:O95382] 0.475357 0.265642454
MAP3K7 0.231972 2427 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 (EC 2.7.1.-) (TRANSFORMING GROWTH FACTOR-BETA-ACTIVATED KINASE 1) (TGF-BETA- ACTIVATED KINASE 1). [SWISSPROT;Acc:O43318] 1.06471 0.217873412
MAP3K7IP1 0.225506 2681 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 INTERACTING PROTEIN 1 (TAK1-BINDING PROTEIN 1). [SWISSPROT;Acc:Q15750] 1.08199 0.208417823
MAP3K7IP2 0.11552 2289 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 INTERACTING PROTEIN 2 ISOFORM 1; TAK1-BINDING PROTEIN 2. [RefSeq;Acc:NM_015093] 0.519559 0.22234241
MAP3K7IP3 0.147358 2286 0.662751 0.222342931
MAP4 0.036083 1895 MICROTUBULE-ASSOCIATED PROTEIN 4 (MAP 4). [SWISSPROT;Acc:P27816] 0.155117 0.232617959
MAPK1 1.33288 696 MITOGEN-ACTIVATED PROTEIN KINASE 1 (EC 2.7.1.37) (EXTRACELLULAR SIGNAL-REGULATED KINASE 2) (ERK-2) (MITOGEN-ACTIVATED PROTEIN KINASE 2) (MAP KINASE 2) (MAPK 2) (P42-MAPK) (ERT1). [SWISSPROT;Acc:P28482] 5.01763 0.265639356
MAPK11 0.0331306 2622 MITOGEN-ACTIVATED PROTEIN KINASE 12 (EC 2.7.1.37) (EXTRACELLULAR SIGNAL-REGULATED KINASE 6) (ERK-6) (ERK5) (STRESS-ACTIVATED PROTEIN KINASE-3) (MITOGEN-ACTIVATED PROTEIN KINASE P38 GAMMA) (MAP KINASE P38 GAMMA). [SWISSPROT;Acc:P53778] 0.157765 0.209999683
MAPK14 0.0434669 2628 MITOGEN-ACTIVATED PROTEIN KINASE 14 (EC 2.7.1.37) (MITOGEN-ACTIVATED PROTEIN KINASE P38ALPHA) (MAP KINASE P38ALPHA) (CYTOKINE SUPPRESSIVE ANTI-INFLAMMATORY DRUG BINDING PROTEIN) (CSAID BINDING PROTEIN) (CSBP) (MAX-INTERACTING PROTEIN 2) (MAP KINASE MXI2) 0.206986 0.209999227
MAPK3 1.11399 679 MITOGEN-ACTIVATED PROTEIN KINASE 3 (EC 2.7.1.37) (EXTRACELLULAR SIGNAL-REGULATED KINASE 1) (ERK-1) (INSULIN-STIMULATED MAP2 KINASE) (MAP KINASE 1) (MAPK 1) (P44-ERK1) (ERT2) (P44-MAPK) (MICROTUBULE- ASSOCIATED PROTEIN-2 KINASE). [SWISSPROT;Acc:P273 4.19348 0.265648101
MAPK8IP3 0.218174 650 C-JUN-AMINO-TERMINAL KINASE INTERACTING PROTEIN 3 (JNK-INTERACTING PROTEIN 3) (JIP-3) (JNK MAP KINASE SCAFFOLD PROTEIN 3) (MITOGEN- ACTIVATED PROTEIN KINASE 8-INTERACTING PROTEIN 3). [SWISSPROT;Acc:Q9UPT6] 0.814576 0.267837501
MAPKAPK2 0.0673673 2629 MAP KINASE-ACTIVATED PROTEIN KINASE 2 (EC 2.7.1.-) (MAPK-ACTIVATED PROTEIN KINASE 2) (MAPKAP KINASE 2) (MAPKAPK-2). [SWISSPROT;Acc:P49137] 0.320798 0.209999127
MAPKAPK3 0.052697 2626 MITOGEN-ACTIVATED PROTEIN KINASE-ACTIVATED PROTEIN KINASE 3; MAPKAP KINASE 3. [RefSeq;Acc:NM_004635] 0.250939 0.209999243
MAPKBP1 0.116954 350 0.41404 0.282470293
MAPRE1 0.109553 1426 MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [SWISSPROT;Acc:Q15691] 0.449228 0.243869483
MAPRE2 0.0850122 1429 "MICROTUBULE-ASSOCIATED PROTEIN, RP/EB FAMILY, MEMBER 2; T-CELL ACTIVATION PROTEIN, EB1 FAMILY; APC-BINDING PROTEIN EB1. [RefSeq;Acc:NM_014268]" 0.348604 0.243864672
MAPRE3 0.0890817 1428 MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 3 (PROTEIN EB3). [SWISSPROT;Acc:Q9UPY8] 0.365289 0.243866363
MARCH1 0.0285481 1881 0.122644 0.232772088
MARCH8 0.0341996 1874 CELLULAR MODULATOR OF IMMUNE RECOGNITION. [RefSeq;Acc:NM_145021] 0.146922 0.232773853
MARK1 0.021031 1462 MAP/MICROTUBULE AFFINITY-REGULATING KINASE 1. [RefSeq;Acc:NM_018650] 0.0865364 0.243030678
MARK2 0.0198288 1466 MAP/MICROTUBULE AFFINITY-REGULATING KINASE 2 ISOFORM B; ELKL MOTIF KINASE 1; ELKL MOTIF KINASE. [RefSeq;Acc:NM_004954] 0.08159 0.243029783
MARS 0.0641898 2494 METHIONYL-TRNA SYNTHETASE (EC 6.1.1.10) (METHIONINE--TRNA LIGASE) (METRS). [SWISSPROT;Acc:P56192] 0.297931 0.2154519
MARS2 0.0914148 2395 0.416755 0.219349018
MAT1A 0.53545 1828 S-ADENOSYLMETHIONINE SYNTHETASE ALPHA AND BETA FORMS (EC 2.5.1.6) (METHIONINE ADENOSYLTRANSFERASE) (ADOMET SYNTHETASE) (MAT-I/III). [SWISSPROT;Acc:Q00266] 2.28647 0.234181949

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/