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.


Navigation/Query Panel:
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Gene Rank description expected Hugo measured final
Results: HTML CSV LaTeX Showing element 3108 to 3157 of 3206 in total
Rank
description
expected
Hugo
measured
final
3108 CYCLIN-DEPENDENT KINASE 2-ASSOCIATED PROTEIN 1 (CDK2-ASSOCIATED PROTEIN 1) (PUTATIVE ORAL CANCER SUPPRESSOR) (DELETED IN ORAL CANCER- 1) (DOC-1). [SWISSPROT;Acc:O14519] 3.36807 CDK2AP1 0.310615 0.09222344
3109 "MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE IB (EC 3.2.1.113) (PROCESSING ALPHA-1,2-MANNOSIDASE IB) (ALPHA-1,2-MANNOSIDASE IB) (MANNOSIDASE ALPHA CLASS 1A MEMBER 2). [SWISSPROT;Acc:O60476]" 1.26306 no value 0.116081 0.091904581
3110 CYTOHESIN 3 (ARF NUCLEOTIDE-BINDING SITE OPENER 3) (ARNO3 PROTEIN) (GENERAL RECEPTOR OF PHOSPHOINOSITIDES 1) (GRP1). [SWISSPROT;Acc:O43739] 0.563976 PSCD3 0.0518319 0.091904443
3111 CYTOHESIN 2 (ARF NUCLEOTIDE-BINDING SITE OPENER) (ARNO PROTEIN) (ARF EXCHANGE FACTOR). [SWISSPROT;Acc:Q99418] 0.565408 PSCD2 0.0519635 0.09190443
3112 CYTOHESIN 1 (SEC7 HOMOLOG B2-1). [SWISSPROT;Acc:Q15438] 0.650054 PSCD1 0.0597428 0.091904365
3113 CYTOHESIN 4. [SWISSPROT;Acc:Q9UIA0] 0.483626 PSCD4 0.0444473 0.091904281
3114 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] 0.2235 NFYA 0.0202662 0.09067651
3115 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] 1.58875 NFYC 0.144062 0.090676318
3116 "LIM DOMAIN PROTEIN, CARDIAC (MUSCLE LIM PROTEIN) (CYSTEINE-RICH PROTEIN 3) (CRP3). [SWISSPROT;Acc:P50461]" 1.14635 CSRP3 0.101174 0.088257513
3117 SMOOTH MUSCLE CELL LIM PROTEIN (CYSTEINE-RICH PROTEIN 2) (CRP2) (LIM-ONLY PROTEIN 5). [SWISSPROT;Acc:Q16527] 1.25295 CSRP2 0.110507 0.088197454
3118 LIKELY ORTHOLOG OF MOUSE SHC SH2-DOMAIN BINDING PROTEIN 1. [RefSeq;Acc:NM_024745] 0.836397 SHCBP1 0.0737653 0.088194123
3119 0.634694 C1orf14 0.0559756 0.088193051
3120 CYSTEINE-RICH PROTEIN 1 (CRP1) (CRP). [SWISSPROT;Acc:P21291] 1.37814 CSRP1 0.121467 0.08813836
3121 THROMBOSPONDIN 3 PRECURSOR. [SWISSPROT;Acc:P49746] 0.775204 THBS3 0.0679913 0.087707623
3122 CARTILAGE OLIGOMERIC MATRIX PROTEIN PRECURSOR (COMP). [SWISSPROT;Acc:P49747] 0.771779 COMP 0.0676858 0.087701013
3123 NUCLEAR DNA-BINDING PROTEIN; SMALL UNIQUE NUCLEAR RECEPTOR COREPRESSOR; C1D DNA-BINDING PROTEIN. [RefSeq;Acc:NM_006333] 0.874459 no value 0.0678638 0.077606612
3124 "EGF-LIKE-DOMAIN, MULTIPLE 7; NEU1 PROTEIN. [RefSeq;Acc:NM_016215]" 1.55221 EGFL7 0.117485 0.075688857
3125 PALMITOYL-PROTEIN THIOESTERASE 2 PRECURSOR (EC 3.1.2.22) (PALMITOYL- PROTEIN HYDROLASE 2) (PPT-2) (G14). [SWISSPROT;Acc:Q9UMR5] 2.05735 EGFL8 0.155614 0.075638078
3126 "BETA-1,4 MANNOSYLTRANSFERASE. [RefSeq;Acc:NM_019109]" 0.785148 ALG1 0.0577935 0.073608415
3127 METALLOPROTEASE 1; METALLOPROTEASE 1 (PITRILYSIN FAMILY). [RefSeq;Acc:NM_014889] 0.781248 PITRM1 0.0574917 0.073589564
3128 MYOSIN VB (MYOSIN 5B) (FRAGMENT). [SWISSPROT;Acc:Q9ULV0] 1.65007 MYO5B 0.113029 0.068499518
3129 1.29368 CC2D1A 0.0886161 0.068499242
3130 MYOSIN VC (MYOSIN 5C). [SWISSPROT;Acc:Q9NQX4] 1.78081 MYO5C 0.121984 0.068499166
3131 "MYOSIN VA (MYOSIN 5A) (DILUTE MYOSIN HEAVY CHAIN, NON-MUSCLE) (MYOSIN HEAVY CHAIN 12) (MYOXIN). [SWISSPROT;Acc:Q9Y4I1]" 2.39209 no value 0.163856 0.068499095
3132 PYRROLINE-5-CARBOXYLATE REDUCTASE (EC 1.5.1.2) (P5CR) (P5C REDUCTASE). [SWISSPROT;Acc:P32322] 2.1027 PYCR1 0.137845 0.06555619
3133 TROPHININ. [SWISSPROT;Acc:Q12816] 1.01402 TRO 0.0662986 0.065381945
3134 MELANOMA-ASSOCIATED ANTIGEN D1 (MAGE-D1 ANTIGEN) (NEUROTROPHIN RECEPTOR-INTERACTING MAGE HOMOLOG) (PRO2292). [SWISSPROT;Acc:Q9Y5V3] 1.01339 MAGED1 0.0662574 0.065381936
3135 "MELANOMA ANTIGEN, FAMILY D, 4 ISOFORM 1; MAGE1 PROTEIN; MAGE-E1 PROTEIN; MAGED4 PROTEIN. [RefSeq;Acc:NM_030801]" 1.01213 MAGED4 0.066175 0.065381917
3136 MAGEB10
3137 MELANOMA-ASSOCIATED ANTIGEN 10 (MAGE-10 ANTIGEN). [SWISSPROT;Acc:P43363] 1.0115 MAGEA10 0.0661338 0.065381908
3138 HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA1. [RefSeq;Acc:NM_020932] 1.02411 no value 0.0669581 0.065381746
3139 25.135 NSMCE4A 1.64337 0.065381739
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 MAGED2 0.0669169 0.065381737
3141 MELANOMA-ASSOCIATED ANTIGEN 6 (MAGE-6 ANTIGEN) (MAGE3B). [SWISSPROT;Acc:P43360] 0.993851 MAGEA6 0.0649797 0.065381732
3142 MELANOMA-ASSOCIATED ANTIGEN 2 (MAGE-2 ANTIGEN). [SWISSPROT;Acc:P43356] 0.990069 MAGEA2B 0.0647324 0.065381706
3143 HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA3. [RefSeq;Acc:NM_138703] 0.987862 MAGEE2 0.0645881 0.065381703
3144 MELANOMA-ASSOCIATED ANTIGEN 8 (MAGE-8 ANTIGEN). [SWISSPROT;Acc:P43361] 0.997949 MAGEA8 0.0652476 0.065381698
3145 MELANOMA-ASSOCIATED ANTIGEN 9 (MAGE-9 ANTIGEN). [SWISSPROT;Acc:P43362] 0.994797 MAGEA9 0.0650415 0.065381681
3146 MELANOMA-ASSOCIATED ANTIGEN 12 (MAGE-12 ANTIGEN) (MAGE12F). [SWISSPROT;Acc:P43365] 0.98408 MAGEA4 0.0643408 0.065381676
3147 MELANOMA-ASSOCIATED ANTIGEN 1 (MAGE-1 ANTIGEN) (ANTIGEN MZ2-E). [SWISSPROT;Acc:P43355] 0.99133 no value 0.0648148 0.065381659
3148 MELANOMA-ASSOCIATED ANTIGEN 3 (MAGE-3 ANTIGEN) (ANTIGEN MZ2-D). [SWISSPROT;Acc:P43357] 0.988493 0.0646293 0.065381647
3149 MELANOMA-ASSOCIATED ANTIGEN 4 (MAGE-4 ANTIGEN) (MAGE-X2) (MAGE-41). [SWISSPROT;Acc:P43358] 0.996058 0.0651239 0.065381634
3150 MELANOMA-ASSOCIATED ANTIGEN C1 (MAGE-C1 ANTIGEN) (CANCER-TESTIS ANTIGEN CT7). [SWISSPROT;Acc:O60732] 0.993221 MAGEC1 0.0649384 0.065381622
3151 MELANOMA-ASSOCIATED ANTIGEN B1 (MAGE-B1 ANTIGEN) (MAGE-XP ANTIGEN) (DSS-AHC CRITICAL INTERVAL MAGE SUPERFAMILY 10) (DAM10). [SWISSPROT;Acc:P43366] 1.02096 MAGEB4 0.066752 0.065381602
3152 "MELANOMA ANTIGEN, FAMILY B, 6. [RefSeq;Acc:NM_173523]" 1.00142 MAGEB6B 0.0654743 0.065381458
3153 NECDIN. [SWISSPROT;Acc:Q99608] NDN
3154 1.00804 MAGEB18 0.0659071 0.065381433
3155 MELANOMA-ASSOCIATED ANTIGEN F1 (MAGE-F1 ANTIGEN). [SWISSPROT;Acc:Q9HAY2] 1.06793 MAGEF1 0.0698227 0.065381345
3156 MELANOMA-ASSOCIATED ANTIGEN 11 (MAGE-11 ANTIGEN). [SWISSPROT;Acc:P43364] 1.00678 MAGEA11 0.0658246 0.065381315
3157 PYRROLINE 5-CARBOXYLATE REDUCTASE ISOFORM. [RefSeq;Acc:NM_013328] 2.02325 PYCR2 0.131587 0.06503744

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/