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:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
expected Gene Rank description measured final Hugo
Results: HTML CSV LaTeX Showing element 2252 to 2301 of 3206 in total
expected
Rank
description
measured
final
Hugo
0.981321 2844 C-TYPE LECTIN SUPERFAMILY MEMBER 1 PRECURSOR (CARTILAGE-DERIVED C-TYPE LECTIN). [SWISSPROT;Acc:O75596] 0.188839 0.192433465 CLEC3A
0.982529 3084 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(T) BETA SUBUNIT 3 (TRANSDUCIN BETA CHAIN 3). [SWISSPROT;Acc:P16520] 0.0979655 0.09970749 GNB3
0.982579 376 PRE-MRNA SPLICING FACTOR PRP17 (HPRP17) (EH-BINDING PROTEIN 3) (EHB3). [SWISSPROT;Acc:O60508] 0.274292 0.279155162 CDC40
0.982761 1394 UBIQUITIN-CONJUGATING ENZYME E2 A (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE A) (UBIQUITIN CARRIER PROTEIN A) (HR6A) (HHR6A). [SWISSPROT;Acc:P49459] 0.240046 0.244256742 UBE2A
0.98408 3146 MELANOMA-ASSOCIATED ANTIGEN 12 (MAGE-12 ANTIGEN) (MAGE12F). [SWISSPROT;Acc:P43365] 0.0643408 0.065381676 MAGEA4
0.985475 1199 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] 0.244748 0.248355362 KCNIP2
0.985597 2899 CELL DIVISION PROTEIN KINASE 3 (EC 2.7.1.-). [SWISSPROT;Acc:Q00526] 0.17249 0.175010679 CDK3
0.986471 548 CUG TRIPLET REPEAT RNA-BINDING PROTEIN 1 (CUG-BP1) (RNA-BINDING PROTEIN BRUNOL-2) (DEADENYLATION FACTOR CUG-BP) (50 KDA NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN) (EDEN-BP). [SWISSPROT;Acc:Q92879] 0.267337 0.271003405 CUGBP1
0.986632 3023 SEPTIN-LIKE PROTEIN KIAA0202 (FRAGMENT). [SWISSPROT;Acc:Q92599] 0.118014 0.119612986 SEPT8
0.987283 759 C1 DOMAIN-CONTAINING PHOSPHATASE AND TENSIN-LIKE PROTEIN ISOFORM 2; PUTATIVE PROTEIN TYROSINE PHOSPHATASE; C1 DOMAIN-CONTAINING PHOSPHATASE AND TENSIN-LIKE PROTEIN; TENSIN 2. [RefSeq;Acc:NM_015319] 0.260485 0.263840257 TENC1
0.987862 3143 HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA3. [RefSeq;Acc:NM_138703] 0.0645881 0.065381703 MAGEE2
0.988036 2238 0.221267 0.223946293 no value
0.988493 3148 MELANOMA-ASSOCIATED ANTIGEN 3 (MAGE-3 ANTIGEN) (ANTIGEN MZ2-D). [SWISSPROT;Acc:P43357] 0.0646293 0.065381647
0.990069 3142 MELANOMA-ASSOCIATED ANTIGEN 2 (MAGE-2 ANTIGEN). [SWISSPROT;Acc:P43356] 0.0647324 0.065381706 MAGEA2B
0.99133 3147 MELANOMA-ASSOCIATED ANTIGEN 1 (MAGE-1 ANTIGEN) (ANTIGEN MZ2-E). [SWISSPROT;Acc:P43355] 0.0648148 0.065381659 no value
0.993221 3150 MELANOMA-ASSOCIATED ANTIGEN C1 (MAGE-C1 ANTIGEN) (CANCER-TESTIS ANTIGEN CT7). [SWISSPROT;Acc:O60732] 0.0649384 0.065381622 MAGEC1
0.993451 3076 TOB1 PROTEIN (TRANSDUCER OF ERBB-2 1). [SWISSPROT;Acc:P50616] 0.102521 0.103196836 TOB1
0.993851 3141 MELANOMA-ASSOCIATED ANTIGEN 6 (MAGE-6 ANTIGEN) (MAGE3B). [SWISSPROT;Acc:P43360] 0.0649797 0.065381732 MAGEA6
0.994797 3145 MELANOMA-ASSOCIATED ANTIGEN 9 (MAGE-9 ANTIGEN). [SWISSPROT;Acc:P43362] 0.0650415 0.065381681 MAGEA9
0.995332 3103 NEUROGENIC DIFFERENTIATION FACTOR 2 (NEUROD2). [SWISSPROT;Acc:Q15784] 0.0917931 0.0922236 NEUROD2
0.996058 3149 MELANOMA-ASSOCIATED ANTIGEN 4 (MAGE-4 ANTIGEN) (MAGE-X2) (MAGE-41). [SWISSPROT;Acc:P43358] 0.0651239 0.065381634 no value
0.996772 1180 MYELIN GENE EXPRESSION FACTOR 2. [RefSeq;Acc:NM_016132] 0.248404 0.249208445 MYEF2
0.996773 2187 U3 SNORNP PROTEIN 4 HOMOLOG. [RefSeq;Acc:NM_033416] 0.225682 0.226412634 IMP4
0.997527 2903 60S RIBOSOMAL PROTEIN L22 (EPSTEIN-BARR VIRUS SMALL RNA ASSOCIATED PROTEIN) (EBER ASSOCIATED PROTEIN) (EAP) (HEPARIN BINDING PROTEIN HBP15). [SWISSPROT;Acc:P35268] 0.173712 0.174142655 no value
0.997879 2508 RAS SUPPRESSOR PROTEIN 1 (RSU-1) (RSP-1). [SWISSPROT;Acc:Q15404] 0.214312 0.214767522 RSU1
0.997949 3144 MELANOMA-ASSOCIATED ANTIGEN 8 (MAGE-8 ANTIGEN). [SWISSPROT;Acc:P43361] 0.0652476 0.065381698 MAGEA8
0.998529 428 PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN (CLATHRIN ASSEMBLY LYMPHOID MYELOID LEUKEMIA PROTEIN). [SWISSPROT;Acc:Q13492] 0.276961 0.27736901 PICALM
0.999179 2902 TYROSINE AMINOTRANSFERASE (EC 2.6.1.5) (L-TYROSINE:2-OXOGLUTARATE AMINOTRANSFERASE) (TAT). [SWISSPROT;Acc:P17735] 0.174557 0.174700429 no value
0.999309 1794 GUANINE DEAMINASE (EC 3.5.4.3) (GUANASE) (GUANINE AMINASE) (GUANINE AMINOHYDROLASE) (GAH) (P51-NEDASIN). [SWISSPROT;Acc:Q9Y2T3] 0.234676 0.234838273 GDA
0.999533 1482 TRANSCRIPTION FACTOR-LIKE PROTEIN MRG15 (MORF-RELATED GENE 15 PROTEIN) (MORTALITY FACTOR 4-LIKE 1) (MSL3-1 PROTEIN) (HSPC008/HSPC061). [SWISSPROT;Acc:Q9UBU8] 0.242846 0.242959462 MORF4L1
0.99966 181 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 2 (EIF-3 BETA) (EIF3 P36) (EIF3I) (TGF-BETA RECEPTOR INTERACTING PROTEIN 1) (TRIP-1). [SWISSPROT;Acc:Q13347] 0.336662 0.336776504 EIF3I
1 2850 DB83 PROTEIN. [SWISSPROT;Acc:P57088] 0.191364 0.191364 TMEM33
2986 AMP DEAMINASE 2 (EC 3.5.4.6) (AMP DEAMINASE ISOFORM L). [SWISSPROT;Acc:Q01433] 0.138195 0.138195 AMPD2
2987 C9orf68
1.00105 2330 RIBOSOMAL PROTEIN S27-LIKE PROTEIN; 40S RIBOSOMAL PROTEIN S27 ISOFORM. [RefSeq;Acc:NM_015920] 0.221494 0.221261675 RPS27L
1.00142 3152 "MELANOMA ANTIGEN, FAMILY B, 6. [RefSeq;Acc:NM_173523]" 0.0654743 0.065381458 MAGEB6B
3153 NECDIN. [SWISSPROT;Acc:Q99608] NDN
1.00248 2924 RAD50 HOMOLOG ISOFORM 1. [RefSeq;Acc:NM_005732] 0.168223 0.167806839 RAD50
1.00293 2941 CHROMOBOX PROTEIN HOMOLOG 5 (HETEROCHROMATIN PROTEIN 1 HOMOLOG ALPHA) (HP1 ALPHA) (ANTIGEN P25). [SWISSPROT;Acc:P45973] 0.15563 0.155175336 CBX5
1.00481 1200 POTASSIUM CHANNEL-INTERACTING PROTEIN 4 ISOFORM 4; CALSENILIN-LIKE PROTEIN. [RefSeq;Acc:NM_147183] 0.249548 0.24835342 KCNIP4
1.00678 3156 MELANOMA-ASSOCIATED ANTIGEN 11 (MAGE-11 ANTIGEN). [SWISSPROT;Acc:P43364] 0.0658246 0.065381315 MAGEA11
1.00804 3154 0.0659071 0.065381433 MAGEB18
1.00989 1130 PHOSPHOLIPID SCRAMBLASE 2 (PL SCRAMBLASE 2) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 2). [SWISSPROT;Acc:Q9NRY7] 0.252989 0.250511442 PLSCR2
1.00996 123 SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1 (SNRNP CORE PROTEIN D1) (SM-D1) (SM-D AUTOANTIGEN). [SWISSPROT;Acc:P13641] 0.36177 0.358202305 SNRPD1
1.00998 1870 "CREATINE KINASE, B CHAIN (EC 2.7.3.2) (B-CK). [SWISSPROT;Acc:P12277]" 0.235164 0.232840254 CKB
1.01082 98 VAV PROTO-ONCOGENE. [SWISSPROT;Acc:P15498] 0.379284 0.375224076 VAV1
1.0115 3137 MELANOMA-ASSOCIATED ANTIGEN 10 (MAGE-10 ANTIGEN). [SWISSPROT;Acc:P43363] 0.0661338 0.065381908 MAGEA10
1.01187 603 ZINC FINGER PROTEIN ZIC 1 (ZINC FINGER PROTEIN OF THE CEREBELLUM 1). [SWISSPROT;Acc:Q15915] 0.272286 0.269091879 ZIC1
1.01194 2951 CYCLIN G2. [SWISSPROT;Acc:Q16589] 0.149439 0.147675752 CCNG2
1.01213 3135 "MELANOMA ANTIGEN, FAMILY D, 4 ISOFORM 1; MAGE1 PROTEIN; MAGE-E1 PROTEIN; MAGED4 PROTEIN. [RefSeq;Acc:NM_030801]" 0.066175 0.065381917 MAGED4

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/